Home      Labs      Publications      People      Tools   

From CAGT

PRECISE Science

PRECISE (Predicted and Consensus Interaction Sites in Enzymes) provides a summary of interactions between the amino acid residues of an enzyme and its various ligands (substrate and transition state analogues, cofactors, inhibitors, and products). In the current version this information is extracted from the enzyme-ligand complexes in the PDB by performing a number of steps as follows.

  1. Clustering homologous enzyme chains. Although enzymes with the same EC number have the same function, they may substantially differ in terms of sequence and/or structure. Since consensus binding sites can be defined only for enzymes with appropriate overlap of their sequences and structures, we have clustered the enzymes in the PDB such that in each cluster the proteins have the same EC number, and all chains are sequence-similar, with a BLAST p-value of 10e-40. The clusters are based on chains rather than the entire protein, since enzymes may have chains of different functions and/or non-homologous chains.

  2. Selecting a representative for each homologous cluster. The chains within a sequence-similar cluster thus derived are automatically ranked according to the precision and completeness of their structural data. The measures of the structural quality are adopted from the NCBI’s Non-Redundant PDB Chain Set (nrpdb), see http://www.ncbi.nlm.nih.gov/Structure/VAST/nrpdb.html

  3. Selecting ligand type. If the PDB file contains a ligand, it is classified as (a) peptide, (b) nucleotide, (c) metal ion, or (d) “other�.

  4. Calculation of hydrogen bonds and non-bonded interactions. The receptor-ligand interactions are determined using the program HBPLUS by Thornton and coworkers (http://www.biochem.ucl.ac.uk/bsm/hbplus/home.html). The results are later parsed and extracted into residue-based formats, giving separate files for each residue that is interacting with the ligand.

  5. Summing all interactions within a cluster for the aligned residues. The number of “hits�, or interactions, for a given residue is calculated automatically throughout the entire cluster. Again, the hits are atom based; two interacting residue can have a hit greater than one if several atoms are involved in the interaction.

  6. Final output. If there are non-homologues chains present in the query pdb, a subsequent page will let users to specify which chain to show. The output page will show the sequence of the representative of the cluster along with different color codes for each residue representing the number of hits. Optional filtersallow users to restrict the output to (a) selected chains in the cluster (b) non-bonded or hydrogen bonding interactions; and (c) selected ligand types.


Protein Engineering