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KMID : 0377220080330040007
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Medical Journal of Chosun Univercity
2008 Volume.33 No. 4 p.7 ~ p.14
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A Brief Introduction to Docking Programs in Drug Design
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Abstract
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A ligand-receptor docking is an important event in biology because it is critically related to the molecular recognition. There have been enorm-ous amount of efforts to improve docking per-formance such as getting correct binding poses, selecting active ligands, and ranking the active ligands correctly. This whole area of docking using computational technology is now mature in the sense that there have been enormous at-tempts have been made to improve docking performance. As a result, various sampling algorithms and scoring functions and their combinations have been tested in more than a dozen of docking program packages. The main accomplishment of last two decades is probably their availability. Among those, Autodock and Dock are freely available for academic users including source code, while Glide, Gold, FlexX, and ICM are commercially available. These programs fully consider ligand flexibility, while partially consider receptor flexibility. There are two main components for any docking program. They are searching (sampling) algorithm and scoring function. Sampling algorithm moves the conformational space and should sample a part conformational space which contain the ‘correct binding pose’. A scoring function needs to guide as well as evaluate the ‘correct binding pose’. Without substantial performance improvement of scoring function for last two decades, research focus has now moved to address computationally demanding receptor flexibility, at least partially. Introduction of receptor-flexibility has been reported to improves the accuracy of binding pose prediction, because some of the receptors are inherently flexible, and previous rigid docking methods cannot be applied for flexible receptors. In this review, various docking programs, current state of the art, and future challenges are briefly described
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KEYWORD
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Docking, Ligand, Receptor, Searching Algorithm, Scoring Function
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