Docking

Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using for example scoring functions. The associations between biologically relevant molecules such as proteins, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore docking is useful for predicting both the strength and type of signal produced. Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Given the biological and pharmaceutical significance of molecular docking, considerable efforts have been directed towards improving the methods used to predict docking.

Further information

1. Косинский Ю.А., Пырков Т.В., Луценко С.В., Ефремов Р.Г. Предсказание структуры комплексов белок-лиганд: от компьютерной модели к биологической функции.// Российский Химический Журнал, (2006) т. L(2), 36-44.
2. Betts M. J., Sternberg M. J. An analysis of conformational changes on protein-protein association: Implication for predictive docking. Protein Eng. (1999) 12, 271-283.
3. Kitchen D. B., Decornez H., Furr, J. R., Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov (2004) 3, 935-949.
4. Totrov M, Abagyan R (April 2008). "Flexible ligand docking to multiple receptor conformations: a practical alternative". Curr. Opin. Struct. Biol. 18 (2): 178–84.
5. Alonso H., Bliznyuk A.A., Gready J.E. Combining docking and molecular dynamic simulations in drug design. Med Res Rev (2006) 26, 531-568.
6. Hartmann C, Antes I, Lengauer T (February 2009). "Docking and scoring with alternative side-chain conformations". Proteins 74 (3): 712–26.
7. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acid Res (2000) 28, 235-242.
8. Статья Docking (molecular) из Wikipedia, свободной энциклопедии. Доступно под лицензией Creative Commons Attribution-Share Alike
9. Статья Молекулярная стыковка из Wikipedia, свободной энциклопедии. Доступно под лицензией Creative Commons Attribution-Share Alike

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