title: PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
abstract: 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.
authors.affiliation: Department of Biomedical Engineering and Program in Bioinformatics, Boston University, CA, USA.
authors.forename: Shu-Hsien
authors.initials: SH
authors.lastname: Sheu
authors.forename: David R
authors.initials: DR
authors.lastname: Lancia
authors.forename: Karl H
authors.initials: KH
authors.lastname: Clodfelter
authors.forename: Melissa R
authors.initials: MR
authors.lastname: Landon
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D016384:Consensus Sequence; D030562:Databases, Protein / Q000639:trends; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D020407:Internet; D008024:Ligands; D017386:Sequence Homology, Amino Acid; D014584:User-Computer Interface
chemical_list: D004798:Enzymes; D008024:Ligands