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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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 > 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.
AbstractList	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 For further resources related to this article, please visit the WIREs website. 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. 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.1298This article is categorized under:Structure and Mechanism > Molecular StructuresComputer and Information Science > VisualizationMolecular and Statistical Mechanics > Molecular Mechanics 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
Author	Yuan, Shuguang Chan, H.C. Stephen Hu, Zhenquan
Author_xml	– sequence: 1 givenname: Shuguang orcidid: 0000-0001-9858-4742 surname: Yuan fullname: Yuan, Shuguang email: shuguang.yuan@gmail.com organization: Ecole Polytechnique Fédérale de Lausanne (EPFL) – sequence: 2 givenname: H.C. Stephen surname: Chan fullname: Chan, H.C. Stephen organization: University of Bradford – sequence: 3 givenname: Zhenquan surname: Hu fullname: Hu, Zhenquan organization: Chinese Academy of Science
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Snippet	PyMOL, a cross‐platform molecular graphics tool, has been widely used for three‐dimensional (3D) visualization of proteins, nucleic acids, small molecules,... PyMOL , a cross‐platform molecular graphics tool, has been widely used for three‐dimensional ( 3D ) visualization of proteins, nucleic acids, small molecules,... PyMOL, a cross-platform molecular graphics tool, has been widely used for three-dimensional (3D) visualization of proteins, nucleic acids, small molecules,...
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SubjectTerms	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
Title	Using PyMOL as a platform for computational drug design
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