title: [Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides].
abstract: Knowledge of 3D-structure of protein-ligand complex is a major prerequisite for understanding the functioning mechanism of cellular proteins and membrane receptors. This is also of a great help in rational drug design projects. In the present paper we briefly review the molecular docking approaches used to predict possible orientation of a ligand in the protein binding site. The recent trends to improve the accuracy and efficiency of docking algorithms are demonstrated with the results obtained in Laboratory of Biomolecular Modeling. Particular attention is paid to protein-ligand hydrophobic and stacking interactions responsible for molecular recognition of ligand fragments. Such type of interactions are not always adequately represented in scoring criteria of docking applications that leads to mismatch in 3D-structure complexes predictions. That is why further inquiry of methods to account for these interactions is now the area of active research.
authors.forename: T V
authors.initials: TV
authors.lastname: Pyrkov
authors.forename: I V
authors.initials: IV
authors.lastname: Ozerov
authors.forename: E D
authors.initials: ED
authors.lastname: Blitskaia
authors.forename: R G
authors.initials: RG
authors.lastname: Efremov
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D008958:Models, Molecular; D009711:Nucleotides / Q000737:chemistry* / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D009711:Nucleotides; D010455:Peptides; D011506:Proteins