Tools and Procedures for Visualization of Proteins and Other Biomolecules

Lurong Pan1, Stephen G. Aller1

1 Department of Pharmacology and Toxicology, Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 19.12
DOI:  10.1002/0471142727.mb1912s110
Online Posting Date:  April, 2015
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Abstract

Protein, peptides, and nucleic acids are biomolecules that drive biological processes in living organisms. An enormous amount of structural data for a large number of these biomolecules has been described with atomic precision in the form of structural “snapshots” that are freely available in public repositories. These snapshots can help explain how the biomolecules function, the nature of interactions between multi‐molecular complexes, and even how small‐molecule drugs can modulate the biomolecules for clinical benefits. Furthermore, these structural snapshots serve as inputs for sophisticated computer simulations to turn the biomolecules into moving, “breathing” molecular machines for understanding their dynamic properties in real‐time computer simulations. In order for the researcher to take advantage of such a wealth of structural data, it is necessary to gain competency in the use of computer molecular visualization tools for exploring the structures and visualizing three‐dimensional spatial representations. Here, we present protocols for using two common visualization tools—the Web‐based Jmol and the stand‐alone PyMOL package—as well as a few examples of other popular tools. © 2015 by John Wiley & Sons, Inc.

Keywords: macromolecular visualization; Jmol; PyMOL; molecular graphics

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Using a Web‐Based Visualization Tool: Jmol
  • Basic Protocol 2: Using Stand‐Alone Visualization Tool: PyMOL
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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