PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes.
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.
Sheu
Shu-Hsien
SH
Department of Biomedical Engineering and Program in Bioinformatics, Boston University, CA, USA.
Lancia
David R
DR
Clodfelter
Karl H
KH
Landon
Melissa R
MR
Vajda
Sandor
S
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
D004798:Enzymes; D008024:Ligands