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
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library


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

PDF or HTML at Wiley Online Library

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
PDF or HTML at Wiley Online Library


PDF or HTML at Wiley Online Library



Literature Cited

Literature Cited
  Berman, H., Henrick, K., and Nakamura, H. 2003. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10:980.
  Goddard, T.D., Huang, C.C., and Ferrin, T.E. 2005. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure 13:473‐482.
  Gosling, J. and McGilton, H. 1996. The Java Language Environment. Oracle Technology Network. Available at‐140151.html.
  Herraez, A. 2006. Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Educ. 34:255‐261.
  Hsin, J., Arkhipov, A., Yin, Y., Stone, J.E., and Schulten, K. 2008. Using VMD: An introductory tutorial. Curr. Protoc. Bioinform. 24:5.7.1–5.7.48.
  Kelch, B.A., Makino, D.L., O'Donnell, M., and Kuriyan, J. 2011. How a DNA polymerase clamp loader opens a sliding clamp. Science 334:1675‐1680.
  Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wyckoff, H., and Phillips, D.C. 1958. A three‐dimensional model of the myoglobin molecule obtained by x‐ray analysis. Nature 181:662‐666.
  Kisielowski, C., Freitag, B., Bischoff, M., van Lin, H., Lazar, S., Knippels, G., Tiemeijer, P., van der Stam, M., von Harrach, S., Stekelenburg, M., Haider, M., Uhlemann, S., Muller, H., Hartel, P., Kabius, B., Miller, D., Petrov, I., Olson, E.A., Donchev, T., Kenik, E.A., Lupini, A.R., Bentley, J., Pennycook, S.J., Anderson, I.M., Minor, A.M., Schmid, A.K., Duden, T., Radmilovic, V., Ramasse, Q.M., Watanabe, M., Erni, R., Stach, E.A., Denes, P., and Dahmen, U. 2008. Detection of single atoms and buried defects in three dimensions by aberration‐corrected electron microscope with 0.5‐A information limit. Microsc. Microanal. 14:469‐477.
  Kleywegt, G.J., Harris, M.R., Zou, J.Y., Taylor, T.C., Wahlby, A., and Jones, T.A. 2004. The Uppsala Electron‐Density Server. Acta Crystallogr. D Biol. Crystallogr. 60:2240‐2249.
  Kwan, A.H., Mobli, M., Gooley, P.R., King, G.F., and Mackay, J.P. 2011. Macromolecular NMR spectroscopy for the non‐spectroscopist. FEBS J. 278:687‐703.
  Li, X., Mooney, P., Zheng, S., Booth, C.R., Braunfeld, M.B., Gubbens, S., Agard, D.A., and Cheng, Y. 2013. Electron counting and beam‐induced motion correction enable near‐atomic‐resolution single‐particle cryo‐EM. Nat. Methods 10:584‐590.
  O'Donoghue, S.I., Goodsell, D.S., Frangakis, A.S., Jossinet, F., Laskowski, R.A., Nilges, M., Saibil, H.R., Schafferhans, A., Wade, R.C., Westhof, E., and Olson, A.J. 2010. Visualization of macromolecular structures. Nat. Methods 7:S42‐55.
  Rossum, G.v. 1995. Python tutorial, Technical Report CS‐R9526. Centrum voor Wiskunde en Informatica (CWI), Amsterdam.
  Schmidt, A., Teeter, M., Weckert, E., and Lamzin, V.S. 2011. Crystal structure of small protein crambin at 0.48 A resolution. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67:424‐428.
  Watson, H.C. 1969. The stereochemistry of the protein myoglobin. Prog. Stereochem. 4:299.
PDF or HTML at Wiley Online Library