VENN, a tool for titrating sequence conservation onto protein structures

Authors

Jay Vyas, University of Connecticut Heath Center,
Michael R. Gryk, University of Connecticut Health Center
Martin R. Schiller, University of Nevada, Las VegasFollow

Document Type

Article

Publication Date

10-2009

Publication Title

Nucleic Acids Research

Volume

37

Issue

18

First page number:

1

Last page number:

5

Abstract

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

Keywords

Amino acid sequence; CCAAT-Enhancer-Binding Protein-beta/chemistry; Conserved Sequence; Fibroblast Growth Factor 8/chemistry; Fibroblast growth factors; Fibroblasts; Humans; Models; Molecular; Proteins—Conformation; Protein Conformation; Sequence Homology; Amino Acid; Software

Disciplines

Biology | Computer Sciences | Life Sciences | Molecular Biology | Structural Biology

Language

English

Creative Commons License

This work is licensed under a Creative Commons Attribution 3.0 License.

Repository Citation

Vyas, J., Gryk, M. R., Schiller, M. R. (2009). VENN, a tool for titrating sequence conservation onto protein structures. Nucleic Acids Research, 37(18), 1-5.
http://dx.doi.org/10.1093/nar/gkp616