Bioinformatics Advance Access originally published online on April 8, 2004
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.
Applications Note |
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces
1 Núcleo de Bioinformática, Centro Nacional de Pesquisa Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil and 2 Laboratório de Bioinformática, Embrapa/Recursos Genéticos e Biotecnologia
Received on September 25, 2003; revised on January 27, 2004; accepted on February 5, 2004
Advance Access Publication April 8, 2004
Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge–charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite.
Availability: http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).
Contact: neshich{at}cbi.cnptia.embrapa.br
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. H. Mealey, J.-H. Lee, S. R. Leib, M. H. Littke, and T. C. McGuire A Single Amino Acid Difference within the {alpha}-2 Domain of Two Naturally Occurring Equine MHC Class I Molecules Alters the Recognition of Gag and Rev Epitopes by Equine Infectious Anemia Virus-Specific CTL J. Immunol., November 15, 2006; 177(10): 7377 - 7390. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Neshich, L. C. Borro, R. H. Higa, P. R. Kuser, M. E. B. Yamagishi, E. H. Franco, J. N. Krauchenco, R. Fileto, A. A. Ribeiro, G. B. P. Bezerra, et al. The Diamond STING server Nucleic Acids Res., July 1, 2005; 33(suppl_2): W29 - W35. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Sobolev, E. Eyal, S. Gerzon, V. Potapov, M. Babor, J. Prilusky, and M. Edelman SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment Nucleic Acids Res., July 1, 2005; 33(suppl_2): W39 - W43. [Abstract] [Full Text] [PDF]
|
|