Nucleic Acids Research Advance Access originally published online on August 5, 2009
Nucleic Acids Research 2009 37(18):e124; doi:10.1093/nar/gkp616
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Nucleic Acids Research, 2009, Vol. 37, No. 18 e124
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
VENN, a tool for titrating sequence conservation onto protein structures
Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030-3305, USA
*To whom correspondence should be addressed. Tel: +1 702 895 3390; Fax: +1 860 895 3956; Email: martin.schiller{at}unlv.edu
Received March 27, 2009. Revised July 1, 2009. Accepted July 8, 2009.
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/.