Bioinformatics, Vol 15, 327-332, Copyright © 1999 by Oxford University Press
V Sobolev, A Sorokine, J Prilusky, EE Abola and M Edelman
MOTIVATION: New software has been designed to assist the molecular
biologist in understanding the structural consequences of modifying a
ligand and/or protein. RESULTS: Tools are described for the analysis of
ligand-protein contacts (LPC software) and contacts of structural units
(CSU software) such as helices, sheets, strands and residues. Our approach
is based on a detailed analysis of interatomic contacts and interface
complementarity. For any ligand or structural unit, these software
automatically: (i) calculate the solvent-accessible surface of every atom;
(ii) determine the contacting residues and type of interaction they undergo
(hydrophobic-hydrophobic, aromatic-aromatic, etc.); (iii) indicate all
putative hydrogen bonds. LPC software further predicts changes in binding
strength following chemical modification of the ligand. AVAILABILITY: Both
LPC and CSU can be accessed through the PDB and are integrated in the 3DB
Atlas page of all PDB files. For any given file, the tools can also be
accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and
http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code
added at the end in each case. Finally, LPC and CSU can be accessed at:
http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.
ARTICLES
Automated analysis of interatomic contacts in proteins
Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il
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