Detailed Information on Publication Record
2005
Molecular Dynamics Study of Protein-Ligand Interactions
KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČABasic information
Original name
Molecular Dynamics Study of Protein-Ligand Interactions
Name in Czech
Studioum interakci protein-ligand pomoci molekulove dynamiky
Authors
KŘÍŽ, Zdeněk (203 Czech Republic, guarantor), Michal OTYEPKA (203 Czech Republic), Iveta BÁRTOVÁ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic)
Edition
Wroclaw, Cellular and Molecular Biology Letters, p. 111-112, 2 pp. 2005
Publisher
Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw
Other information
Language
English
Type of outcome
Stať ve sborníku
Field of Study
10403 Physical chemistry
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
RIV identification code
RIV/00216224:14310/05:00013838
Organization unit
Faculty of Science
ISBN
1425-8153
Keywords in English
Molecular Dynamics; Interaction Energy; Cyclin Dependent Kinase; Olomoucine; Roscovitine; Bohemine
Tags
Změněno: 19/7/2005 13:32, Mgr. Zdeněk Kříž, Ph.D.
V originále
Detailed knowledge of interactions inside the proteins plays an important role in drug design. Experimental methods such as X-crystallography, NMR spectroscopy and neutron diffraction are typical experimental methods to analyze these interactions at atomic level. These experimental methods can, in some cases, be complemented by molecular modeling methods. The molecular docking combined with flexible conformational search, molecular dynamics and quantum dynamics are the most used modeling methods at this time. Recently, the interactions of solvent molecules with cyclin dependent kinase (CDK2) using molecular dynamics were studied in our laboratory [1]. The previous study was extended by including solvation into interaction energies between protein and ligands acording to ref. [2]. Our molecular dynamics study was performed on complexes of cyclin-dependent kinase CDK2 with natural substrate ATP and with inhibitors roscovitine, olomoucine [3] and olomoucine II [4]. The X-ray crystallographic data was used as starting points for molecular dynamics study performed by the AMBER program suite [5]. The composition of van der Waals and electrostatic interactions between the CDK2 and ligand, including interactions between CDK2, ligand and solvent molecules, were calculated along the MD trajectories.
In Czech
Detailed knowledge of interactions inside the proteins plays an important role in drug design. Experimental methods such as X-crystallography, NMR spectroscopy and neutron diffraction are typical experimental methods to analyze these interactions at atomic level. These experimental methods can, in some cases, be complemented by molecular modeling methods. The molecular docking combined with flexible conformational search, molecular dynamics and quantum dynamics are the most used modeling methods at this time. Recently, the interactions of solvent molecules with cyclin dependent kinase (CDK2) using molecular dynamics were studied in our laboratory [1]. The previous study was extended by including solvation into interaction energies between protein and ligands acording to ref. [2]. Our molecular dynamics study was performed on complexes of cyclin-dependent kinase CDK2 with natural substrate ATP and with inhibitors roscovitine, olomoucine [3] and olomoucine II [4]. The X-ray crystallographic data was used as starting points for molecular dynamics study performed by the AMBER program suite [5]. The composition of van der Waals and electrostatic interactions between the CDK2 and ligand, including interactions between CDK2, ligand and solvent molecules, were calculated along the MD trajectories.
Links
| MSM0021622413, plan (intention) |
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