Efficiency of tabu-search-based conformational search algorithms

✍ Scribed by Christoph Grebner; Johannes Becker; Svetlana Stepanenko; Bernd Engels

• Publisher: John Wiley and Sons
• Year: 2011
• Tongue: English
• Weight: 571 KB
• Volume: 32
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.21807

✦ Synopsis

Abstract

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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011