Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume 22, Issue 11, Pages 815-829Publisher
SPRINGER
DOI: 10.1007/s10822-008-9216-5
Keywords
peptide docking; mean field technique; MOLS sampling; computational drug design
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Funding
- Department of Biotechnology, Government of India [BT/PR5476/BID/07/136/2004]
- University Grants Commission
- Department of Science and Technology, Government of India
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The theoretical prediction of the association of a flexible ligand with a protein receptor requires efficient sampling of the conformational space of the ligand. Several docking methodologies are currently available. We propose a new docking technique that performs well at low computational cost. The method uses mutually orthogonal Latin squares to efficiently sample the docking space. A variant of the mean field technique is used to analyze this sample to arrive at the optimum. The method has been previously applied to explore the conformational space of peptides and identify structures with low values for the potential energy. Here we extend this method to simultaneously identify both the low energy conformation as well as a 'high-scoring' docking mode. Application of the method to 56 protein-peptide complexes, in which the length of the peptide ligand ranges from three to seven residues, and comparisons with Autodock 3.05, showed that the method works well.
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