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Automated analysis of interatomic contacts in proteins
V Sobolev1, A Sorokine, J Prilusky
1Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il
Bioinformatics (Oxford, England)
|May 13, 1999
Summary
New software, ligand-protein contacts (LPC) and contacts of structural units (CSU), helps molecular biologists understand structural changes. These tools analyze interatomic contacts and predict binding strength modifications.
Area of Science:
- Structural Biology
- Computational Biology
- Biochemistry
Background:
- Understanding the structural impact of ligand and protein modifications is crucial in molecular biology.
- Existing tools may lack comprehensive analysis of ligand-protein interactions and structural unit contacts.
Purpose of the Study:
- To introduce novel software, ligand-protein contacts (LPC) and contacts of structural units (CSU), for analyzing molecular structures.
- To provide tools that assist in understanding the structural consequences of modifying ligands and proteins.
Main Methods:
- Development of LPC software for analyzing ligand-protein interactions.
- Development of CSU software for analyzing contacts within structural units (helices, sheets, strands, residues).
- Utilizing detailed analysis of interatomic contacts and interface complementarity.
Main Results:
- Both LPC and CSU automatically calculate solvent-accessible surfaces and identify contacting residues and interaction types.
- The software indicates all putative hydrogen bonds.
- LPC software predicts changes in binding strength after ligand modification.
Conclusions:
- LPC and CSU software offer valuable insights into ligand-protein interactions and structural modifications.
- These tools are accessible via the Protein Data Bank (PDB) and dedicated websites, facilitating their use in research.