Using PyMOL as a platform for computational drug design

PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing, and making movies. This Python‐based softw...

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Published in:Wiley interdisciplinary reviews. Computational molecular science Vol. 7; no. 2
Main Authors: Yuan, Shuguang, Chan, H.C. Stephen, Hu, Zhenquan
Format: Journal Article
Language:English
Published: Hoboken, USA Wiley Periodicals, Inc 01.03.2017
Wiley Subscription Services, Inc
Subjects:
Computation
Computer applications
Computer simulation
Design
Drug development
Drug screening
Drugs
Graphics
Mechanics
Modelling
Molecular modelling
Molecular structure
Nucleic acids
Proteins
Ray tracing
Software
Statistical mechanics
Utilities
Visualization
ISSN:1759-0876, 1759-0884
Online Access:Get full text
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Summary:PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing, and making movies. This Python‐based software, alongside many Python plugin tools, has been developed to enhance its utilities and facilitate the drug design in PyMOL. To gain an insightful view of useful drug design tools and their functions in PyMOL, we present an extensive discussion on various molecular modeling modules in PyMOL, covering those for visualization and analysis enhancement, protein–ligand modeling, molecular simulations, and drug screening. This review provides an excellent introduction to present 3D structures visualization and computational drug design in PyMOL. WIREs Comput Mol Sci 2017, 7:e1298. doi: 10.1002/wcms.1298 This article is categorized under: Structure and Mechanism > Molecular Structures Computer and Information Science > Visualization Molecular and Statistical Mechanics > Molecular Mechanics The in situ drug design in PyMOL, guided by the predicted hydration sites in the binding pocket.
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ISSN:1759-0876
1759-0884
DOI:10.1002/wcms.1298