AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott,Arthur J. Olson +1 more
TLDR
AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development.Abstract:
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 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.read more
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Journal ArticleDOI
UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Thomas D. Goddard,Conrad C. Huang,Elaine C. Meng,Eric F. Pettersen,Gregory S. Couch,John H. Morris,Thomas E. Ferrin +6 more
TL;DR: This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility in ChimeraX.
Journal ArticleDOI
Molecular docking: a powerful approach for structure-based drug discovery.
TL;DR: This review presents a brief introduction of the available molecular docking methods, and their development and applications in drug discovery, and a recently developed local move Monte Carlo based approach is introduced.
Book ChapterDOI
Small-Molecule Library Screening by Docking with PyRx
Sargis Dallakyan,Arthur J. Olson +1 more
TL;DR: This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems.
Journal ArticleDOI
Ligand docking and binding site analysis with PyMOL and Autodock/Vina.
Daniel Seeliger,Bert L. de Groot +1 more
TL;DR: An interface between the popular molecular graphics system PyMOL and the molecular docking suites Autodock and Vina is presented and it is demonstrated how the combination of docking and visualization can aid structure-based drug design efforts.
Journal ArticleDOI
Unravelling the Role of O-glycans in Influenza A Virus Infection
Juliane Mayr,Kam Lau,Jimmy C. C. Lai,Ivan A. Gagarinov,Yun Shi,Sarah McAtamney,Renee W. Y. Chan,John M. Nicholls,Mark von Itzstein,Thomas Haselhorst +9 more
TL;DR: It is suggested that sialylated Galβ(1,3)GalNAc as O-glycan core 1 glycoforms are involved in the influenza A virus life cycle and play a particularly crucial role during infection of HPAI strains.
References
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.