ProSMoS

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Introduction:	Programs that assess structural similarity compare two structures to each other and define common regions. Structural classification experts look for a particular structural motif instead. Most programs base similarity scores on superposition and closeness of either coordinates or contacts. Experts pay more attention to the orientation of the main chain and general match of secondary structural elements. We developed a program that emulates an expert. Starting from a structure, the program delineates secondary structural elements. A matrix of element interactions (parallel or antiparallel) and handedness of connections is constructed. All structures are reduced to matrices that contain just enough information to define a fold, so the definition is general and large deviations in coordinates are tolerated. A user supplies a matrix for a motif, and ProSMoS lists all structures that exactly match this motif. Resulting hits can be post-processed with several scripts and may be mapped to SCOP or can be visualized in PyMOL.
Reference:	Shi S, Zhong Y, Majumdar I, Sri Krishna S, Grishin NV. Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinformatics. 2007 Jun 1;23(11):1331-8 Shuoyong Shi, Bhadrachalam Chitturi and Nick V. Grishin. ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W526-31
Services:	a. Pattern search by query matrix: Search for structure pattern with user-defined query matrix against PDB or SCOP b. Pattern search by query structure: Search for structure pattern with a query protein strcutre against PDB or SCOP
Examples:	Precomputed results for eight common structure patterns.
Availability:	Standalone ProSMoS and related post-processing scripts can be downloaded from here. Databases of metamatrices constructed on PDB and SCOP can be downloaded from here.

Updated on July 08, 2009