The protein flexibility in receptor-ligand docking simulations
نویسندگان
چکیده
منابع مشابه
The protein flexibility in receptor-ligand docking simulations
Many small-molecule drugs work by binding specifically to a target protein in the cell. It is known for over a century that both the ligand and protein receptor change their conformation in the association process, which is called the induced-fit effect. Ligand conformational change is routinely treated in methods for insilico drug discovery, because typical drug molecules have seldom more than...
متن کاملReceptor flexibility in de novo ligand design and docking.
One of the major problems in computational drug design is incorporation of the intrinsic flexibility of protein binding sites. This is particularly crucial in ligand binding events, when induced fit can lead to protein structure rearrangements. As a consequence of the huge conformational space available to protein structures, receptor flexibility is rarely considered in ligand design procedures...
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Inspired by the current representation of the ligand-receptor binding process, a normal-mode-based methodology is presented to incorporate receptor flexibility in ligand docking and virtual screening. However, the systematic representation of the deformation space grows geometrically with the number of modes, and furthermore, midscale loop rearrangements like those found in protein kinase bindi...
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Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and ligand-bound states, the conformational flexibility of the protein is typically ignored in protein-small molecule docking programs. We previously described the program RosettaLigand, which leverage...
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Acknowledgements I would like to start by thanking Prof. Meir Edelman and Dr. Vladimir Sobolev for their guidance and the high level of scientific independence they trusted in me. A different posture would not have permitted my full development as a free thinker. I would like to thank Professors Ron Unger and Amnon Horovitz for their valuable comments throughout this work as assigned readers of...
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ژورنال
عنوان ژورنال: Journal of Cheminformatics
سال: 2010
ISSN: 1758-2946
DOI: 10.1186/1758-2946-2-s1-o11