Nucleic Acids Research, 2005, Vol. 33, Database issue D206-D211
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
Department of Biomedical Engineering and 1 Program in Bioinformatics, Boston University, CA, USA
* To whom correspondence should be addressed. Tel: +1 617 353 4757; Fax: +1 617 353 6766; Email: vajda{at}bu.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received August 13, 2004; Revised and Accepted October 12, 2004
PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its ligands (substrate and transition state analogs, cofactors, inhibitors and products). It is available online at http://precise.bu.edu/. In the current version, all information on interactions is extracted from the enzyme–ligand complexes in the Protein Data Bank (PDB) by performing the following steps: (i) clustering homologous enzyme chains such that, in each cluster, the proteins have the same EC number and all sequences are similar; (ii) selecting a representative chain for each cluster; (iii) selecting ligand types; (iv) finding non-bonded interactions and hydrogen bonds; and (v) summing the interactions for all chains within the cluster. The output of the search is the color-coded sequence of the representative. The colors indicate the total number of interactions found at each amino acid position in all chains of the cluster. Clicking on a residue displays a detailed list of interactions for that residue. Optional filters allow restricting the output to selected chains in the cluster, to non-bonded or hydrogen bonding interactions, and to selected ligand types. The binding site information is essential for understanding and altering substrate specificity and for the design of enzyme inhibitors.
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