Selective Flexibility of Side-Chain Residues Improves VEGFR-2 Docking Score using AutoDock Vina
نویسندگان
چکیده
منابع مشابه
Selective flexibility of side-chain residues improves VEGFR-2 docking score using AutoDock Vina.
Selective side-chain residue flexibility is an option available on AutoDock Vina docking software. This approach is promising as it attempts to provide a more realistic ligand-protein interaction environment without an unmanageable increase in computer processing time. However, studies validating this approach are still scarce. VEGFR-2 (vascular endothelial growth factor receptor 2), a known pr...
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BACKGROUND Cross-docking is an approach to find the best holo structures among multiple structures available for a target protein. RESULTS CrossDocker significantly decreases the time needed for setting parameters and inputs for performing multiple dockings, data collection and subsequent analysis. CONCLUSION CrossDocker was written in Python language and is available as executable binary f...
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Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms ...
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Conventional rigid docking algorithms have been unsatisfactory in their computational results, largely due to the fact that protein structures are flexible in live environments. In response, we propose to introduce the side-chain flexibility in protein motif into the docking. First, the Morse theory is applied to curvature labeling and surface region growing, for segmentation of the protein sur...
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ژورنال
عنوان ژورنال: Chemical Biology & Drug Design
سال: 2012
ISSN: 1747-0277
DOI: 10.1111/j.1747-0285.2011.01313.x