Active Site Recognition in Proteases

This server finds all aminoacids on the surface of a protease. Based on geometrical criteria it tries to find all possible active sites. The server recognizes active sites in: serine, cysteine, aspartic, metallo- and glutamic proteases. Server produces rasmol script that can be used for displaying active site residues by rasmol/chime or jmol programs.

Two parameters are used in the process of recognizing geometrical arrangement of residues in the active sites:

1) R - probe radius (default 1.4A) used for creating surface around the molecule. The smaller value of R the more penetrating surface is created. The surface is created my molsurf program. The algorithm becomes less stable for values lower than 1.1A. In most cases R = 1.4-1.3A is sufficient.

2) tol - geometrical tolerance (default 0.1A) for distances between amino acid atoms in the active site. For most cases use: 0.1-0.4A. For very bad model higher value for tol can be used.

The protein binding pockets are predicted with Putative Active Sites with Spheres - PASS program developed by G.Patrick Brady, Jr., and Pieter F.W.Stouten while at DuPont Pharmaceutical Company. The PASS algorithm is designed to fill the cavities in a protein structure using spheres. The largest spheres are the best guesses for the active sites.

In most cases calculations should not take more than 30 seconds. Well characterized active site should have low value of Zscore (between 0.0-0.6) and high value of Score (>0.8)

This tool performs calculations on either uploaded local PDB file or downloaded from RCSB file if PDB id code is provided.

AS paper
molsurf program
PASS program