TY - JOUR T1 - Classification of protein disulphide-bridge topologies JF - J Comput Aided Mol Des Y1 - 2001 A1 - Mas, J. M. A1 - Aloy, P. A1 - M. A. Marti-Renom A1 - Oliva, B. A1 - de Llorens, R. A1 - Aviles, F. X. A1 - Querol, E. KW - Algorithms Computer Simulation Databases as Topic Disulfides/*chemistry Models KW - Molecular Protein Structure KW - Secondary Protein Structure KW - Tertiary Proteins/*chemistry/*classification Software AB - The preferential occurrence of certain disulphide-bridge topologies in proteins has prompted us to design a method and a program, KNOT-MATCH, for their classification. The program has been applied to a database of proteins with less than 65% homology and more than two disulphide bridges. We have investigated whether there are topological preferences that can be used to group proteins and if these can be applied to gain insight into the structural or functional relationships among them. The classification has been performed by Density Search and Hierarchical Clustering Techniques, yielding thirteen main protein classes from the superimposition and clustering process. It is noteworthy that besides the disulphide bridges, regular secondary structures and loops frequently become correctly aligned. Although the lack of significant sequence similarity among some clustered proteins precludes the easy establishment of evolutionary relationships, the program permits us to find out important structural or functional residues upon the superimposition of two protein structures apparently unrelated. The derived classification can be very useful for finding relationships among proteins which would escape detection by current sequence or topology-based analytical algorithms. VL - 15 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11394740 N1 - Mas, J M Aloy, P Marti-Renom, M A Oliva, B de Llorens, R Aviles, F X Querol, E Comparative Study Research Support, Non-U.S. Gov’t Netherlands Journal of computer-aided molecular design J Comput Aided Mol Des. 2001 May;15(5):477-87. ER -