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Database for three dimensional structures of pepsin‐like enzymes using the internal coordinate system
Author(s) -
Russ A.,
Pechik I.,
Andreeva N.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20612
Subject(s) - pepsin , enzyme , database , superposition principle , chemistry , computer science , computational biology , biochemistry , mathematics , biology , mathematical analysis
A database for 3D structures of pepsin‐like enzymes has been created on the basis of a novel approach using the Internal Coordinate System (ICS). It allows rapid comparison of multiple structures of pepsin‐like enzymes without the need for preliminary calculations. Atomic displacements measured by this approach are very close to those estimated by the superposition procedures widely employed in comparing three‐dimensional structures of proteins. Any new structure of pepsin‐like enzyme converted to the ICS automatically becomes superimposed with all structures in a database. The ICS approach can be used for any class of enzymes and is especially efficient for families containing a large number of homologous structures. Proteins 2005. © 2005 Wiley‐Liss, Inc.