Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 32, Issue 10, Pages 2245-2253Publisher
WILEY
DOI: 10.1002/jcc.21807
Keywords
conformational search; global optimization; Tabu search; basin hopping; simulated annealing; Monte Carlo with minimization
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Funding
- DFG (Deutsche Forschungsgemeinschaft) [SFB 630]
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Efficient conformational search or sampling approaches play an integral role in molecular modeling, leading to a strong demand for even faster and more reliable conformer search algorithms. This article compares the efficiency of a molecular dynamics method, a simulated annealing method, and the basin hopping (BH) approach (which are widely used in this field) with a previously suggested tabu-search-based approach called gradient only tabu search (GOTS). The study emphasizes the success of the GOTS procedure and, more importantly, shows that an approach which combines BH and GOTS outperforms the single methods in efficiency and speed. We also show that ring structures built by a hydrogen bond are useful as starting points for conformational search investigations of peptides and organic ligands with biological activities, especially in structures that contain multiple rings. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2245-2253, 2011
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