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VENN, a tool for titrating sequence conservation onto protein structures.

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/.

Pubmed ID: 19656955

Authors

  • Vyas J
  • Gryk MR
  • Schiller MR

Journal

Nucleic acids research

Publication Data

October 20, 2009

Associated Grants

  • Agency: NIAID NIH HHS, Id: AI078708
  • Agency: NIBIB NIH HHS, Id: EB001496
  • Agency: NIGMS NIH HHS, Id: GM079689

Mesh Terms

  • Amino Acid Sequence
  • CCAAT-Enhancer-Binding Protein-beta
  • Conserved Sequence
  • Fibroblast Growth Factor 8
  • Humans
  • Models, Molecular
  • Protein Conformation
  • Sequence Homology, Amino Acid
  • Software