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WIREs Comput Mol Sci
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Using PyMOL as a platform for computational drug design

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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
Representations of macromolecules and the anaglyph stereo mode in PyMOL. (a) PyMOL can display macromolecules in different styles including lines, sticks, spheres, surface, mesh, dots, ribbon, and carton. (b) The binding pocket of the green fluorescent protein (pdb: 1EMA) displayed in nonstereo cartoon and mesh. (c) The binding pocket of the green fluorescent protein (pdb: 1EMA) displayed in anaglyph stereo mode. The stereo effect can be visualized by a pair of red–blue anaglyph stereo glasses.
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Exemplified plugins in PyMOL. (a) Protein–ligand interaction of Adenosine 2A receptor (A2AR, pdb: 4EIY) generated by the PLIP plugin. Gray stick: A2AR sidechain; green stick: ligand molecule; black dash: hydrophobic contact; cyan dash: H‐bond interaction; yellow dash: ion lock interaction; blue dash: water bridge; and green dash: π–π stacking. (b) The anisotropic network models (ANM) movements of A2AR (pdb: 4EIY) generated by the PyANM plugin. Gray arrow: ANM movement directions. (c) The predicted hydration sites by the WATsite tool for the μ‐opioid receptor (μOR). The hydration sites are shown as small spheres and colored according to their desolvation energy ΔG values. Yellow stick: a morphine molecule in the binding pocket. Green stick: μOR sidechain. Red→Cyan→Green→Blue represents ΔG values range from favorable to unfavorable values. When designing new drug candidates, additional function groups can be introduced in these regions with unfavorable ΔG values, to increase the ligand binding affinity.
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The interface of PyMOL and the workflow of modern computational drug design. Upper panel: The PyMOL interface of main menu and that of the macromolecular builder tools. Lower panel: the workflow of modern computational drug design.
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Molecular and Statistical Mechanics > Molecular Mechanics
Structure and Mechanism > Molecular Structures

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