Video on VENN VENN is an integrative computer program, written by Jay Vyas, for mapping protein sequence conservation among homologues onto a three dimensional structure of a protein (Vyas et al., 2009). VENN was named after John VENN, the inventor of VENN diagrams, because VENN can be used to explore the interaction of sequence and structure to identify important functional regions in proteins, The only input needed in a VENN analysis is an experimental or model PDB structure identifier (e.g. 1EX4). An alternative site for structure models can be found here . VENN retrieves and interprets the PDB file to identify different structure chains. Protein sequences with sequence similarity to each chain are automatically retrieved from the EBI and a list of up to 500 such sequences is presented to the user. The user selects sequences using canned strategies or by their own ad hoc selections. VENN then aligns the protein sequences, calculates a heatmap for conservation of each amino acid position and plots the heatmap onto the protein structure. Different strategies for selecting groups of sequences can be used to identify functional regions and specificity determinants in gene families.

Do to changes in the data access at EBI, the stand alone version of VENN no longer functions and has been deprecated. This has been replaced by a web version of VENN that contains all of the critical functions reported in the publication. VENN was built by Jay Vyas.

PLEASE CITE USE OF VENN WITH THIS PAPER:
Vyas J, Gryk MR, and Schiller. (2009). Venn, a tool for titrating sequence conservation onto protein structures. Nucleic Acids Res., 37, e124. PMID: 19656955