Using <scp>PyMOL</scp> as a platform for computational drug design

TLDR

PyMOL is a cross‑platform molecular graphics tool widely used for 3D visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories, and it also supports molecule editing, ray tracing, and movie creation. The authors aim to enhance PyMOL’s utilities and facilitate drug design by developing Python‑based software and plugins. They discuss various PyMOL modules for visualization, analysis, protein–ligand modeling, simulations, and drug screening. The review offers a comprehensive introduction to 3D structure visualization and computational drug design in PyMOL. The article is published in WIREs Computational Molecular Science 2017, 7:e1298 (doi:10.1002/wcms.1298).

Abstract

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 &gt; Molecular Structures Computer and Information Science &gt; Visualization Molecular and Statistical Mechanics &gt; Molecular Mechanics