Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening
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 کاملUtility of scoring function customization in docking-based virtual screening approaches
Govardhan A. Balaji, Vitukudi N. Balaji and Shashidhar N. Rao* Department of Chemistry, St Joseph’s College, 36 Langford Road, Bangalore 560 027, India Structure Directed Molecular Design, Jubilant Biosys Ltd, #96, Industrial Suburb II Stage, Yeshwantpur, Bangalore 560 022, India Tripos – A CertaraTM Company, 1699 South Hanley Road, St Louis MO 63144, USA Present address: Department of Chemistr...
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...
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ژورنال
عنوان ژورنال: PLOS ONE
سال: 2016
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0155183