AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina
نویسندگان
چکیده
منابع مشابه
AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina
BACKGROUND Halogen bonding has recently come to play as a target for lead optimization in rational drug design. However, most docking program don't account for halogen bonding in their scoring functions and are not able to utilize this new approach. In this study a new and improved halogen bonding scoring function (XBSF) is presented along with its implementation in the AutoDock Vina molecular ...
متن کاملAutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 deve...
متن کامل1001 Ways to run AutoDock Vina for virtual screening
Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides experience with the molecular docking tool itself, the scientist needs to learn how to run it on high-...
متن کاملCrossDocker: a tool for performing cross-docking using Autodock Vina
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...
متن کاملAutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.
Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these wat...
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ژورنال
عنوان ژورنال: Journal of Cheminformatics
سال: 2016
ISSN: 1758-2946
DOI: 10.1186/s13321-016-0139-1