C8855 Advanced Molecular Modelling Methods

Faculty of Science
Spring 2024
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 19. 2. to Sun 26. 5. Wed 9:00–9:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge of quantum chemistry is an advantage. It is strongly suggested that the student go first through the courses C7790 Introduction to Molecular Modelling or C9087 Computational Chemistry for Structural Biology.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The course is aimed at acquiring advanced knowledge in the field of computational chemistry. Its orientation is strongly application-oriented. The course will discuss the methods needed to build models for simulations of predominantly biomolecular systems. Basic problems of incomplete experimental structures and the appropriateness of using artificial intelligence tools to predict structures will be discussed. The preparation of pre-reaction complexes for studying enzymatic reactions and basic methods for studying reaction mechanisms will also be discussed.
Learning outcomes
The student will gain advanced knowledge to study the dynamics and reactivity of biomolecular systems using molecular modelling tools.
Syllabus
  • Basic requirements for models of biomolecular systems * Limitation of experimental (X-ray, NMR, CryoEM) and predicted (AlphaFold2, ESM-Fold, RoseTTAFold2) structures * Ionizable groups and the effect of pH on the model * Docking of substrates into the active site * How to solvate biomolecular systems correctly * Types of water and ion models * Molecular dynamics (MD) of biomolecular systems * Analysis of MD trajectories * Hybrid QM/MM description of the active site of an enzymatic reaction * Calculation of reaction profiles * Study of reaction mechanisms
Literature
  • Encyclopedia of computational chemistry. Edited by Paul von R. Schleyer. Chichester: John Wiley & sons, 1998, xxix, 812. ISBN 047196588X. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
  • JENSEN, Frank. Introduction to computational chemistry. Third edition. Chichester: Wiley, 2017, xxii, 638. ISBN 9781118825990. info
Teaching methods
Lectures combined with discussions.
Assessment methods
The course ends with a written test followed by an optional oral examination.
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2025.

C8855 Advanced Molecular Modelling Methods

Faculty of Science
Spring 2025
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic level of general and physical chemistry. A basic knowledge of quantum chemistry is an advantage. It is strongly suggested that the student go first through the courses C7790 Introduction to Molecular Modelling or C9087 Computational Chemistry for Structural Biology.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The course is aimed at acquiring advanced knowledge in the field of computational chemistry. Its orientation is strongly application-oriented. The course will discuss the methods needed to build models for simulations of predominantly biomolecular systems. Basic problems of incomplete experimental structures and the appropriateness of using artificial intelligence tools to predict structures will be discussed. The preparation of pre-reaction complexes for studying enzymatic reactions and basic methods for studying reaction mechanisms will also be discussed.
Learning outcomes
The student will gain advanced knowledge to study the dynamics and reactivity of biomolecular systems using molecular modelling tools.
Syllabus
  • Basic requirements for models of biomolecular systems * Limitation of experimental (X-ray, NMR, CryoEM) and predicted (AlphaFold2, ESM-Fold, RoseTTAFold2) structures * Ionizable groups and the effect of pH on the model * Docking of substrates into the active site * How to solvate biomolecular systems correctly * Types of water and ion models * Molecular dynamics (MD) of biomolecular systems * Analysis of MD trajectories * Hybrid QM/MM description of the active site of an enzymatic reaction * Calculation of reaction profiles * Study of reaction mechanisms
Literature
  • Encyclopedia of computational chemistry. Edited by Paul von R. Schleyer. Chichester: John Wiley & sons, 1998, xxix, 812. ISBN 047196588X. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
  • JENSEN, Frank. Introduction to computational chemistry. Third edition. Chichester: Wiley, 2017, xxii, 638. ISBN 9781118825990. info
Teaching methods
Lectures combined with discussions.
Assessment methods
The course ends with a written test followed by an optional oral examination.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024.

C8855 Advanced Molecular Modelling Methods

Faculty of Science
Spring 2023
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Ivo Durník, Ph.D. (seminar tutor)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Wed 9:00–9:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Learning outcomes
Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2024, Spring 2025.

C8855 Advanced Molecular Modelling Methods

Faculty of Science
Spring 2022
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Ivo Durník, Ph.D. (seminar tutor)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Wed 9:00–9:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Learning outcomes
Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2021
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 1. 3. to Fri 14. 5. Thu 10:00–10:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Learning outcomes
Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2020
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer)
Guaranteed by
RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Wed 9:00–9:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Learning outcomes
Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2019
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
spring 2018
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2017
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2016
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 10:00–10:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2015
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 10:00–10:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2014
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 10:00–10:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2013
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 10:00–10:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2012
Extent and Intensity
1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Fri 10:00–10:50 C04/118
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2011
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Timetable
Thu 9:00–9:50 C04/211
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2010
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Timetable
Fri 11:00–11:50 C04/211
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2009
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Timetable
Fri 9:00–9:50 C04/211
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives
The course is oriented to obtaining basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2008
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2007
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Timetable
Tue 13:00–13:50 C04/211
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 23 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2006
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 23 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2005
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 23 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2004
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (seminar tutor)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2003
Extent and Intensity
1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 23 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2002
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 23 fields of study the course is directly associated with, display
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
spring 2012 - acreditation

The information about the term spring 2012 - acreditation is not made public

Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2011 - only for the accreditation
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives
At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
Syllabus
  • 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Teaching methods
Lectures combined with discussions.
Assessment methods
Oral examination
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.

C8855 Computational Chemistry and Molecular Modeling II

Faculty of Science
Spring 2008 - for the purpose of the accreditation
Extent and Intensity
1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
Teacher(s)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Prerequisites
Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 21 fields of study the course is directly associated with, display
Course objectives (in Czech)
Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
Syllabus (in Czech)
  • 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
Literature
  • Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
  • JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
  • HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
  • FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
Assessment methods (in Czech)
Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2011 - only for the accreditation, Spring 2002, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (recent)