Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-848d4c4894-nmvwc Total loading time: 0 Render date: 2024-07-04T22:01:53.182Z Has data issue: false hasContentIssue false

13 - Protein Structure Visualization, Comparison, and Classification

Published online by Cambridge University Press:  05 June 2012

Jin Xiong
Jin Xiong
Affiliation:
Texas A & M University
Get access

Summary

Once a protein structure has been solved, the structure has to be presented in a three-dimensional view on the basis of the solved Cartesian coordinates. Before computer visualization software was developed, molecular structures were represented by physical models of metal wires, rods, and spheres. With the development of computer hardware and software technology, sophisticated computer graphics programs have been developed for visualizing and manipulating complicated three-dimensional structures. The computer graphics help to analyze and compare protein structures to gain insight to functions of the proteins.

PROTEIN STRUCTURAL VISUALIZATION

The main feature of computer visualization programs is interactivity, which allows users to visually manipulate the structural images through a graphical user interface. At the touch of a mouse button, a user can move, rotate, and zoom an atomic model on a computer screen in real time, or examine any portion of the structure in great detail, as well as draw it in various forms in different colors. Further manipulations can include changing the conformation of a structure by protein modeling or matching a ligand to an enzyme active site through docking exercises.

Because a Protein Data Bank (PDB) data file for a protein structure contains only x, y, and z coordinates of atoms (see Chapter 12), the most basic requirement for a visualization program is to build connectivity between atoms to make a view of a molecule.

Type
Chapter
Information
Essential Bioinformatics , pp. 187 - 199
Publisher: Cambridge University Press
Print publication year: 2006

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bourne, P. E., and Shindyalov, I. N. 2003. “Structure comparison and alignment.” In Structural Bioinformatics, edited by Bourne, P. E. and Weissig, H., 321–37. Hoboken, NJ: Wiley-LissCrossRefGoogle Scholar
Carugo, O., and Pongor, S. 2002. Recent progress in protein 3D structure comparison. Curr. Protein Pept. Sci. 3:441–9CrossRefGoogle ScholarPubMed
Hadley, C., and Jones, D. T. 1999. A systematic comparison of protein structure classifications: SCOP, CATH, and FSSP. Structure 7:1099–112CrossRefGoogle ScholarPubMed
Jawad, Z., and Paoli, M. 2002. Novel sequences propel familiar folds. Structure 10:447–54CrossRefGoogle ScholarPubMed
Kinch, L. N., and Grishin, N. V. 2002. Evolution of protein structures and functions. Curr. Opin. Struct. Biol. 12:400–8CrossRefGoogle ScholarPubMed
Koehl, P. 2001. Protein structure similarities. Curr. Opin. Struct. Biol. 11:348–53CrossRefGoogle ScholarPubMed
Orengo, C. A., Pearl, F. M. G., and Thornton, J. M. 2003. “The CATH domain structure database.” In Structural Bioinformatics, edited by Bourne, P. E. and Weissig, H., 249–71. Hoboken, NJ: Wiley-LissCrossRefGoogle Scholar
Ouzounis, C. A., Coulson, R. M., Enright, A. J., Kunin, V., and Pereira-Leal, J. B. 2003. Classification schemes for protein structure and function. Nat. Rev. Genet. 4:508–19CrossRefGoogle ScholarPubMed
Reddy, B. J. 2003. “Protein structure evolution and the scop database.” In Structural Bioinformatics, edited by Bourne, P. E. and Weissig, H., 239–48. Hoboken, NJ: Wiley-LissCrossRef
Russell, R. B. 2002. Classification of protein folds. Mol. Biotechnol. 20:17–28CrossRefGoogle ScholarPubMed
Tate, J. 2003. “Molecular visualization.” In Structural Bioinformatics, edited by Bourne, P. E. and Weissig, H., 135–58. Hoboken, NJ: Wiley-LissCrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×