Masarykova univerzita

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Filtrování publikací

    2008

    1. SVOZIL, Daniel, Judit SPONER, Ivan MARCHAN, Alberto PEREZ, Thomas CHEATHAM, Ferda FORTI, Javier LUQUE, Modesto OROZCO a Jiri SPONER. Geometrical and Electronic Structure Variability of the Sugar-phosphate Backbone in Nucleic Acids. Journal of Physical Chemistry B. 2008, roč. 112, č. 27, s. 8188–8197. ISSN 1520-6106.
    2. MISHRA, Navnit Kumar, Petr KULHÁNEK, Lenka ŠNAJDROVÁ, Martin PETŘEK, Anne IMBERTY a Jaroslav KOČA. Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides. Proteins: Structure, Function, and Bioinformatics. Wiley, 2008, roč. 72, č. 1, s. 382–392. ISSN 0887-3585.

    2007

    1. WIESNER, Jiří, Zdeněk KŘÍŽ a Jaroslav KOČA. Alternative entrances into the acetylcholinesterase active site. In Strukturní biofyzika makromolekul II. 2007.
    2. MACEK, Pavel, Petr NOVÁK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation. Journal of Physical Chemistry B. USA: The American Chemical Society, 2007, roč. 111, č. 20, s. 5731-5739. ISSN 1089-5639.
    3. ŠPONER, Jiří. Computational studies of nucleic acids, advances and failures. In Modeling Interactions in Biomolecules III. Praha: Mff UK, Praha, 2007. s. 51.
    4. RÁZGA, Filip, Jaroslav KOČA, Ali MOKDAD a Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Research. Oxford, UK: Oxford Press, 2007, roč. 35, č. 12, s. 4007–4017. ISSN 0305-1048.
    5. RÁZGA, Filip, Jaroslav KOČA a Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: Molecular dynamics study. In Strukturní biofyzika makromolekul II. první. Brno: Brno, 2007. s. 14-14.
    6. ŠPONER, Jiří. Molecular dynamics simulations of quadruplex DNA. In First international meeting on quadruplex DNA,. Louisville, USA: Louisville, USA, 2007. s. 20.
    7. BERSHTEIN, Vladimir A., Larisa M. EGOROVA, Pavel N. YAKUSHEV, Vladimír ŠINDELÁŘ, Petr SYSEL, Tatiana E. SUKHANOVA, Irina P. DOBROVOLSKAYA, Anatoly I. GRIGORIEV, Sotiria KRIPOTOU a Polycarpos PISSIS. Poly(imide-amide)-poly(ethylene glycol) hybrid networks: nanostructure, molecular dynamics and membrane properties. Polymer Bulletin. Germany: Springer, 2007, roč. 58, č. 1, s. 65-74. ISSN 0170-0839.
    8. ŠPONER, Jiří, Ali MOKDAD, Filip RÁZGA, Kamila RÉBLOVÁ a Naděžda ŠPAČKOVÁ. Ribosomal RNA motifs and segments have salient flexibilities. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007. s. 632-633. ISSN 0006-3525.
    9. RÉBLOVÁ, Kamila, Filip LANKAS a Jiri SPONER. Study of structure, dynamics and local elasticity of 16S rRNA Helix 44 using molecular dynamics methods. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007. s. 635-635. ISSN 0006-3525.
    10. WIESNER, Jiří, Zdeněk KŘÍŽ a Jaroslav KOČA. Tryptophane as a Rotating Flap: Omega Loop Dynamics in Acetylcholinesterase. In Modeling Interactions in Biomolecules III. 2007.

    2006

    1. SKLENÁŘ, Vladimír. Dynamics of Protein-Ligand Interactions. In Frontieres of Biomolecular NMR. Lubjlana: Narodna i univerzitetna knjižnica, Ljubljana, 2006. s. 41-41. ISBN 961-6104-08-X.
    2. MATOUŠEK, Jiří, Petr KULHÁNEK, Michal ČAJAN a Jaroslav KOČA. Effect of Solvation on Pinched Cone-Pinched Cone Interconversion of Tetraethoxycalix[4]arene and Tetraethoxythiacalix[4]arene. Journal of Physical Chemistry A. 2006, roč. 110, č. 3, s. 861-867. ISSN 1089-5639.
    3. ŠPAČKOVÁ, Naděžda a Jiří ŠPONER. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Research. Oxford University Press, 2006, roč. 34, č. 2, s. 697-708. ISSN 0006-3465.
    4. MACEK, Pavel, Petr NOVÁK, Hana KŘÍŽOVÁ, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Molecular dynamics study of major urinary protein-pheromone interactions: A structural model for ligand-induced flexibility increase. FEBS Letters. Amsterdam: Elsevier Science B.V., 2006, roč. 580, č. 1, s. 682-684. ISSN 0014-5793.
    5. SVOZIL, Dan, Jiří ŠPONER, Thomas E CHEATHAM a Modesto OROZCO. On the problem with long MD simulations of nucleic acids. In 2006 ISQBP president's meeting. Strasbourg: Strasbourg, 2006. s. 42-42.
    6. NOVÁK, Petr, Pavel MACEK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. PAIN: Program for Analysis of Internal motioN, An Application to MD Simulated Motions of Major Urinary Protein-I. Materials Structure in Chemistry, Biology, Physics and Technology. Praha, 2006, roč. 13, č. 1, s. 31-31. ISSN 1211-5894.
    7. RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA a Jiří ŠPONER. RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics. Structure. USA: CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB, 2006, roč. 14, č. 5, s. 825-835, 10 s. ISSN 0969-2126.
    8. MOKDAD, Ali, Maryna KRASOVSKA, Jiří ŠPONER a Neocles B. LEONTIS. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Research. Oxford University Press, 2006, roč. 34, č. 5, s. 1326-1341. ISSN 0006-3465.
    9. ŠPONER, Jiří. Structure and dynamics of functional RNAs: 3 microseconds of explicit solvent MD. In 2006 ISQBP president's meeting. Strasbourg: Strasbourg, 2006. s. 41-41.
    10. RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA a Jiří ŠPONER. Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations. Biopolymers. USA: Wiley InterScience, 2006, roč. 82, č. 5, s. 504-520. ISSN 0006-3525.
    11. RHODES, Maria, Kamila REBLOVA, Walter NILS a Jiri SPONER. Trapped water molecules are essential to structural dynamics and function of a ribozyme. The Proceedings of the National Academy of Sciences. USA: National Academy of Sciences of the USA, 2006, roč. 103, č. 36, s. 13380-13385. ISSN 1091-6490.

    2005

    1. ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Computer Simulations on Glycosyltransferases Beauties and Pitfalls. In Eurocarb XIII. Bratislava: AV, 2005. s. 24-24.
    2. OTYEPKA, Michal, Iveta BÁRTOVÁ, Zdeněk KŘÍŽ a Jaroslav KOČA. Dynamics of human CDK2 and CDK5 studied by computer simulations. In Cellular and Molecular Biology Letters. Wroclaw: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw, 2005. s. 116-117. ISBN 1425-8153.
    3. OTYEPKA, Michal, Iveta BÁRTOVÁ, Zdeněk KŘÍŽ a Jaroslav KOČA. Dynamika regulačních enzymů buněčných procesů CDK2 a CDK5 studovaná molekulovou dynamikou. In ChemZi. Bratislava: Slovenská chemická spoločnosť, 2005. s. 277-277. ISBN 1336 - 7242.
    4. ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Glycosyltransferase LgtC Active Site Hydration and Role of the Solvent in Substrate Binding. In Strukturní biofyzika makromolekul. Dubrovnik: ICS, 2005. s. 32-32.
    5. ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Glycosyltransferase LgtC Active Site Hydration and Role of the Solvent in Substrate Binding. In Glycoproteomics - protein modifications for versatile functions. Dubrovnik: Dubrovnik, 2005. s. 62-62.
    6. RÁZGA, Filip, Jaroslav KOČA, Jiří ŠPONER a Neocles B. LEONTIS. Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases. Biophysical Journal. USA: Biophysical Society, 2005, roč. 88, č. 5, s. 3466-3485. ISSN 0006-3495.
    7. FADRNÁ, Eva, Klára HLADEČKOVÁ a Jaroslav KOČA. Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2005, roč. 23, č. 2, s. 151-162. ISSN 0739-1102.
    8. BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ a Jaroslav KOČA. Molecular Dynamics Simulations on Cyclin Dependent Kinase 2. Solvent Behavior Analysis and Activation and Inhibition by Phosphorylation -Tools to Design New Inhibitors and Contribute to Understanding Mechanism. In WATOC 2005. Modeling Structure and Reactivity. Cape Town: WATOC 2005., 2005. s. 83-83.
    9. KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ a Jaroslav KOČA. Molecular Dynamics Study of Protein-Ligand Interactions. In Cellular and Molecular Biology Letters. Wroclaw: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw, 2005. s. 111-112. ISBN 1425-8153.
    10. WIESNER, Jiří, Zdeněk KŘÍŽ, Kamil KUČA, Daniel JUN a Jaroslav KOČA. Počítačové modelování a simulace - nové technologie při vývoji prostředkůproti chemickým bojovým látkám. Voj. zdrav. listy. Hradec Králové: Univerzita obrany, 2005, roč. 74, 5/6, s. 171-177. ISSN 0372-7025.
    11. RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA a Jiří ŠPONER. RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function. In Strukturní biofyzika makromolekul. prvé. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005. s. 17-17.
    12. RÁZGA, Filip, Jaroslav KOČA, Neocles B LEONTIS a Jiří ŠPONER. RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance. In Workshop on Modeling Interactions in Biomolecules II. prve. Praha: Praha, 2005. s. p37, 2 s.
    13. WIESNER, Jiří, Zdeněk KŘÍŽ a Jaroslav KOČA. Structure and dynamics of sarin-inhibited acetylcholinesterase. In Strukturní biofyzika makromolekul. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005. s. 21-21.
    14. WIESNER, Jiří, Zdeněk KŘÍŽ a Jaroslav KOČA. Structure and dynamics of sarin-inhibited acetylcholinesterase. In Modeling Interactions in Biomolecules II. Praha: Univerzita Karlova, Praha, 2005. s. 1-1.
    15. MATOUŠEK, Jiří, Petr KULHÁNEK, Michal ČAJAN a Jaroslav KOČA. The Role of Solvation in The Pinched Cone - Pinched Cone Interconversion. In Calix, 8th International Conference on Calixarenes. Praha: Institute of Chemical Technology Prague, 2005. s. P75, 1 s.

    2004

    1. BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ a Jaroslav KOČA. A Molecular Dynamics Study of the Cyclin-Dependent Kinase-2 (CDK2) with Substrate Peptide (HHASPRK), Inhibition of CDK2 by Phosphorylation. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2004. s. 42-43. ISBN 1211 - 5894.
    2. KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ a Jaroslav KOČA. Analysis of CDK2 active-site hydration: A method to design new inhibitors. Proteins: Structure, Function, and Bioinformatics. Wiley, 2004, roč. 55, č. 3, s. 258-274. ISSN 0887-3585.
    3. NOVÁK, Petr a Pavel MACEK. Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., 2004, roč. 11, č. 1, s. 51-51. ISSN 1211-5894.
    4. NOVÁK, Petr, Pavel MACEK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I. In Abstract of the VIth Central European NMR Symposium. Linz: Institut fur Organische Chemie der Johannes Keppler Universitat, Linz, Austria, 2004. s. 20-20.
    5. ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Computational Study of Galactosyltransferase LgtC in Complex with Manganese Ion and Donor Substrate. In Cukrblik 2004: Current Chemistry and Biochemistry of Saccharides. Praha: Ústav chemie přírodních látek VŠCHT, 2004. s. 6-6.
    6. KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ a Jaroslav KOČA. Detailed study of interactions between small molecules and proteins using molecular modeling. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2004. s. 47-47. ISBN 1211 - 5894.
    7. RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER a Neocles B. LEONTIS. Dynamics of Flexible RNA Hinges Relevant to Ribosome Function: non-Watson-Crick basepairs, modular building and specific hydration of RNA Kink-turns. In Materials Structure in Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2004. s. 28. ISBN 1211-5894.
    8. MATOUŠEK, Jiří, Michal ČAJAN, Petr KULHÁNEK a Jaroslav KOČA. Flexibility of Calix[4]arene Skeleton: A Molecular Dynamics Study. In Modelling and Design of Molecular Materials, Book of Abstracts. Wroclaw (Polsko): Wroclaw University of Technology, Poland, 2004. s. L-25, 1 s.
    9. ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Glycosyltransferase LgtC: MD Simulations under Physiological and Non-physiological Conditions. In 22nd International Carbohydrate Symposium. Glasgow: International Carbohydrate Organisation, 2004. s. P388, 1 s.
    10. MACEK, Pavel, Petr NOVÁK, Hana KŘÍŽOVÁ, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. INCREASED DYNAMICS OF MUP-I IN PRESENCE OF LIGAND: EVIDENCE FROM MD SIMULATION AND NMR SPIN RELAXATION. In VIII. Pracovní setkání biochemiků a molekulárních biologů. Brno: Masarykova universita v Brně Přírodovědecká fakulta a Česká společnost pro biochemii a molekulární biologii, 2004. s. 31-31.
    11. ŠNAJDROVÁ, Lenka, Anne IMBERTY, Petr KULHÁNEK a Jaroslav KOČA. MD Simulation of Glycosyltransferase LgtC in Water and in Solution of NaCl. In GlycoT 2004. Le Touquet, France: University of Lille, France, 2004. s. 117-117.
    12. ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. Carbohydrate Research. 2004, roč. 339, č. 5, s. 995-1006. ISSN 0008-6215.
    13. FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jaroslav KOČA, Thomas E. CHEATHAM a Jiří ŠPONER. Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations. Biophysical Journal. Bethesda, USA: Biophysical Society, 2004, roč. 87, č. 1, s. 227-242. ISSN 0006-3495.
    14. ŠNAJDROVÁ, Lenka, Jaroslav KOČA a Anne IMBERTY. Molecular Dynamics Simulations on Glycosyltrasferase LgtC. In Materials Structure in Chemistry. Praha: Czech and Slovak Crystallographic Association, 2004. s. 52-52.
    15. RÁZGA, Filip, Naďa ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2004, roč. 22, č. 2, s. 183-193. ISSN 0739-1102.

    2003

    1. KOČA, Jaroslav. Are Force Fields Able to Predict Coordination Number of Metal Ions in Metalloproteins. In Modeling Interactions in Biomolecules, Workshop. Nove Hrady: Praha, 2003. s. 31-31.
    2. FADRNÁ, Eva a Jaroslav KOČA. Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2003, roč. 20, č. 5, s. 715-731. ISSN 0739-1102.
    3. KOČA, Jaroslav, Chang-Guo ZHAN, Robert RITTENHOUSE a Rick ORNSTEIN. Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. Journal of Computational Chemistry. New York: John Wiley & Sons, 2003, roč. 24, č. 3, s. 368-378. ISSN 0192-8651.
    4. ŠTEFL, Richard, Thomas E. CHEATHAM, Naděžda ŠPAČKOVÁ, Eva FADRNÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamics Analysis of the Substates. Biophysical Journal. Bethesda, USA: Biophysical Society, 2003, roč. 85, č. 3, s. 1787-1804. ISSN 0006-3495.
    5. RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Judit ŠPONER, Jaroslav KOČA a Jiři ŠPONER. Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research. Oxford University Press, 2003, roč. 31, č. 23, s. 6942-6952. ISSN 0006-3465.
    6. ŠNAJDROVÁ, Lenka, Jaroslav KOČA a Anne IMBERTY. Molecular dynamics simulations on glycosyltransferase LgtC. In 12th European Carbohydrate Symposium. Grenoble: CERMAV-CNRS, 2003. s. 398-398.
    7. LEPŠÍK, Martin, Zdeněk KŘÍŽ a Zdeněk HAVLAS. Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2003. s. 23-23. ISBN 1211 - 5894.
    8. TRANTÍREK, Lukáš, Erik CAHA a Radovan FIALA. NMR Relaxation Studies of Fast Internal Motions in Nucleic Acids. In Materials Structure. 1. vyd. Prague: Czech and Slovak Crystalographic Association, 2003. s. 40-41. ISBN 1211-5894.
    9. RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER a Neocles, B. LEONTIS. Structure and Dynamics of RNA K-turn Motifs. In RNA klub. vyd. Praha: Praha, 2003. s. 21-21.
    10. RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER a Neocles, B LEONTIS. Structure And Dynamics Of RNA K-Turn Motifs. In Workshop on Modeling Interactions in Biomolecules : Programme and Book of Abstract. vyd. Praha: Praha, 2003. s. 41-41.

    2002

    1. OTYEPKA, Michal, Zdeněk KŘÍŽ a Jaroslav KOČA. Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations. Journal of Biomolecular Structure & Dynamics. GUILDERLAND: ADENINE PRESS, 2002, roč. 20, č. 2, s. 141-154. ISSN 0739-1102.
    2. OTYEPKA, Michal a Jiří DAMBORSKÝ. Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. Protein Science. 2002, roč. 11, č. 5, s. 1206-1217. ISSN 0961-8368.
    3. KŘÍŽ, Zdeněk, Michal OTYEPKA a Jaroslav KOČA. Hydratace aktivniho mista enzymu CDK2. Studium pomoci molekulove dynamiky. In Chemicke listy 6. Praha: 54. Sjezd chemickych spolecnosti, 2002. s. 424.
    4. KŘÍŽ, Zdeněk, Michal OTYEPKA a Jaroslav KOČA. Hydration of the CDK2 active site. Molecular dynamics study. In Watoc'02 Book of Abstracts. ETH Zurich: WATOC'02, 2002. s. PC439, 1 s.
    5. BÁRTOVÁ, Iveta, Zdeněk KŘÍŽ, Michal OTYEPKA a Jaroslav KOČA. Molecular Dynamics Simulations of CDK2/ATP Complex. In Chemicke listy 6. Praha: 54. Sjezd chemickych spolecnosti, 2002. s. 427.
    6. KŘÍŽ, Zdeněk, Michal OTYEPKA a Jaroslav KOČA. Molecular Modeling of Peptides and Proteins at National Centre for Biomolecular Research (NCBR). In Materials Structure in Chemistry, Biology, Physics and Technology. Praha: 1. setkani ceskych a slovenskych strukturnich biologu, 2002. s. 41-42.

    2001

    1. PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA a Anne IMBERTY. Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations. Biopolymers. John Wiley & Sons, Inc, 2001, roč. 58, č. 7, s. 617-635. ISSN 0006-3525.

    2000

    1. PETROVÁ, Pavla, Jaroslav KOČA a Anne IMBERTY. Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-glucose. Molecular Simulations. 2000, roč. 24, č. 1, s. 325-330.
    2. ŠPAČKOVÁ, Naděžda, Imre BERGER a Jiří ŠPONER. Molecular Dynamics Simulations of Four-stranded Nucleic Acid Structures: i-DNA and G-DNA. In Biochemistry and molecular biology an the threshold of a new century. 1. vyd. Brno: Masarykova univerzita, 2000. s. 90. ISBN 80-210-2266-3.

    1999

    1. ŠPAČKOVÁ, Naděžda, Imre BERGER a Jiří ŠPONER. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1999, roč. 121, č. 23, s. 5519-5534. ISSN 0002-7863.

    1998

    1. ŠPAČKOVÁ, Naděžda, Imre BERGER, Martin EGLI a Jiří ŠPONER. Molecular Dynamics of Hemiprotonated Intercalated Four-stranded i-DNA and Guanine Quartets. Stable Trajectories on a Nanosecond Scale. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., 1998, roč. 5, s. 420. ISSN 1211-5894.
    2. ŠPAČKOVÁ, Naděžda, Imre BERGER, Martin EGLI a Jiří ŠPONER. Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: stable trajectories on a nanosecond scale. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1998, roč. 120, č. 24, s. 6147-6151. ISSN 0002-7863.
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