Section 25.1.8.7.  PASS

PASS (Putative Active Sites with Spheres; Brady & Stouten, 2000) is a simple computational tool that uses geometry to characterize regions of buried volume in proteins and to identify positions likely to represent binding sites based upon the size, shape and burial extent of these volumes. PASS's utility as a predictive tool for binding-site identification was tested by predicting known binding sites of proteins in the PDB using both complexed macromolecules and their corresponding apoprotein structures. The results indicated that PASS can serve as a front-end to fast docking. The main utility of PASS lies in the fact that it can analyse a moderate-size protein (∼30 kDa) in under 20 s, which makes it suitable for interactive molecular modelling, protein-database analysis and aggressive virtual screening efforts. As a modelling tool, PASS: (1) rapidly identifies favourable regions of the protein surface; (2) simplifies visualization of residues modulating binding in these regions; and (3) provides a means of directly visualizing buried volume, which is often inferred indirectly from curvature in a surface representation. PASS produces output in the form of standard PDB files, which are suitable for any modelling package, and provides script files to simplify visualization in Cerius2, Insight II (Section 25.1.7.3), MOE, QUANTA (Section 25.1.7.8), RasMol (Section 25.1.9.6) and SYBYL (Section 25.1.7.9).

Location: http://www.ccl.net/cca/software/UNIX/pass/overview.shtml . Operating systems: SGI, SUN and LINUX. Type: binary. Distribution: free.