Active Site Recognition in Proteases
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AS paper molsurf program PASS program |
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Active Site Recognition in Proteases |
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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.
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Two parameters are used in the process of recognizing geometrical arrangement of residues in the active sites:
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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.
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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.
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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.
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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)
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This tool performs calculations on either uploaded local PDB file or downloaded from RCSB file if PDB id code is provided.
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