Automated analysis of interatomic contacts in proteins.

Clicks: 3
ID: 303847
1999
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Abstract
Abstract 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.
Reference Key
openalex_W2151550848 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors V. M. Sobolev, Anatoly Sorokin, Jaime Prilusky, Enrique E. Abola, Marvin Edelman
Journal BMC Bioinformatics
Year 1999
DOI
10.1093/bioinformatics/15.4.327
URL
https://doi.org/10.1093/bioinformatics/15.4.327
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