Exploring the conformational space of cyclic peptides by a stochastic search method.
作者： Anwar Rayan , Hanoch Senderowitz , Amiram Goldblum
DOI: 10.1016/J.JMGM.2003.12.012
关键词:
摘要: Abstract A stochastic search algorithm is applied in order to probe the conformations of cyclic peptides. The conducted two stages. In first stage, random are generated and evaluated by a penalty function for ring closure ability, following stepwise construction each amino acid into peptide choice one its allowed conformations. conformational ranges backbone dihedral angles have been extracted from Data Bank diverse proteins. Values that do not contribute favorably scoring retained or discarded statistical test. up point which all remaining combinations constructed, scored, sorted, clustered. second side chains added fast optimization was set “united atoms” approach, with “Kollman forcefield” Sybyl 6.8. This iterative elimination finds global minimum most best results, when compared full exhaustive appropriately sized problems. larger problems, we compare results experimental structures. root mean square deviation (RMSD) our crystal structures peptides sizes 4 15 acids mostly below 1.0 A 8 mers under 2.0 A
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