Bi9410 Structural Biology

Faculty of Science
Autumn 2024
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Taught in person.
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Ondřej Vávra, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
The course is taught annually.
The course is taught: every week.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

Bi9410 Structural Biology

Faculty of Science
Autumn 2023
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Taught in person.
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Ondřej Vávra, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Tue 15:00–16:50 B11/305
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2022
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Taught in person.
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Ondřej Vávra, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 14:00–15:50 B11/305
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
autumn 2021
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Taught in person.
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Ondřej Vávra, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 14:00–15:50 B11/305
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2020
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Taught partially online.
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Ondřej Vávra, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 14:00–15:50 prace doma
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2019
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
Mgr. Martina Damborská (assistant)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 14:00–15:50 B11/305
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2018
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
Mgr. Martina Damborská (assistant)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 24. 9. to Fri 14. 12. Wed 14:00–15:50 B11/305
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
autumn 2017
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
Mgr. Martina Damborská (assistant)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 18. 9. to Fri 15. 12. Wed 14:00–15:50 B11/305
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2016
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 19. 9. to Sun 18. 12. Thu 11:00–12:50 B11/235
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2015
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
Mgr. Martina Damborská (assistant)
doc. Mgr. David Bednář, Ph.D. (seminar tutor)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 13:00–14:50 B11/306
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2014
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Mgr. Eva Šebestová, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 15:00–16:50 B11/235
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2013
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Mgr. Martina Damborská (assistant)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: Mgr. Jan Brezovský, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 16. 9. to Fri 6. 12. Wed 12:00–13:50 B11/235
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
On successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Teaching methods
lectures
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2012
Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Mgr. Eva Šebestová, Ph.D. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Wed 12:00–13:50 B11/235
Prerequisites
Knowledge on the level of basic lectures of biochemistry or molecular 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
there are 65 fields of study the course is directly associated with, display
Course objectives
The aim of this course is to introduce the biological systems from the point of view of biomacromolecular structures.
Students will get an overview of methods for determination, retrieval and visualisation of structures, and learn how to infer useful information about their function. Students will also learn basics of important biological phenomena such as protein dynamics or protein-protein, protein-DNA and protein-ligand interactions. At the end of the course, an application of structural biology to the study of molecular basis of essential biological processes, drug design and engineering of novel biocatalysts will be introduced.
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – deposition, retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interacions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interacions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interacions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
Teaching methods
lectures
Assessment methods
written test
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2011

The course is not taught in Autumn 2011

Extent and Intensity
1/0. 1 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jan Brezovský, Ph.D. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The aim of this course is to introduce students into the biological systems from the point of view of biomacromolecular structures.
Students will obtain overview of structure determination, retrieval, visualisation and analysis in order to infer useful information about their function. Students will also learn basics of important biological phenomena such as protein dynamics or protein-protein, protein-DNA and protein-ligand interactions. At the end of the course, an application of structural biology to study molecular basis of essential biological processes, drug design and engineering of novel biocatalysts.
Syllabus
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – deposition, retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Prediction of structure of macromolecular complexes.
  • 5. Dynamics of macromolecules – analysis of molecular dynamics; databases.
  • 6. Protein-protein complexes – evaluation of complex, analysis of interacions; databases.
  • 7. Protein-DNA complexes – evaluation of complex, analysis of interacions; databases.
  • 8. Protein-ligand complexes – evaluation of complex, analysis of interacions; databases.
  • 9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
Teaching methods
lectures
Assessment methods
2 written tests
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

Bi9410 Structural Biology

Faculty of Science
Autumn 2011 - acreditation

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity
2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives (in Czech)
Seznámit studenty s pohledem na biologické systémy z hlediska struktury biologických makromolekul. Strukturní biologie je vědní disciplína odvozená z molekulární biologie, biochemie a biofyziky. Zabývá se molekulární strukturou biologických makromolekul, především proteinů a nukleových kyselin, které jsou nezbytnými komponentami všech živých organismů. Umožňuje určovat tuto strukturu a studovat jak souvisí s biologickou funkcí.
Studenti se naučí, jak se struktury určují, kde je lze získat, jak je zobrazit a následně analyzovat za účelem získání informací o jejich funkci. Dále budou představeny důležité fenomény strukturní biologie – dynamika proteinů, protein-proteinové, protein-DNA a protein-ligandové interakce. V závěr předmětu budou diskutovány aplikace strukturní biologie při studiu důležitých biologických fenoménů na molekulární úrovni, design nových léčiv a biokatalyzátorů.
Syllabus (in Czech)
  • 1. Struktura biologických makromolekul – složení, metody stanovení, využití v biologii.
  • 2. Databáze experimentálních struktur – depozice, získání a hodnocení struktur makromolekul, strukturní databáze PDB, PDBsum, EDS, NDB.
  • 3. Vizualizace struktur – možnosti zobrazení, dostupné programy.
  • 4. Modely struktur – databáze modelů, metody hodnoceni kvality modelů, příprava modelů.
  • 5. Predikce struktury makromolekulárních komplexů.
  • 6. Analýza struktury proteinu – identifikace důležitých regionů: vazebná/aktivní místa, transportní cesty, flexibilní regiony, katalytické aminokyseliny.
  • 7. Dynamika makromolekul – analýza dynamiky a její databáze.
  • 8. Komplexy protein-protein – hodnocení komplexu, analýza interakcí a jejich databáze.
  • 9. Komplexy protein-DNA – hodnocení komplexu, analýza interakcí a jejich databáze.
  • 10. Komplexy protein-ligand – hodnocení komplexu, analýza interakcí a jejich databáze.
  • 11. Modifikace struktury proteinu – stanovení vlivu mutace na strukturu a funkci proteinu.
  • 12. Aplikace strukturní biologie – biologický výzkum, hledání nových léčiv, design biokatalyzátorů.
Literature
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Teaching methods (in Czech)
teoretická příprava fromou přednášky
Assessment methods (in Czech)
písemný test
Language of instruction
Czech
Follow-Up Courses
Further Comments
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
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