A Modified Valley Restrained Monte Carlo Method to Efficiently Search the Low Energy Structures of Peptides |
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| Authors: | Chong Chul Chai Seung Hoon Choi Mu Shik Jhon |
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| Affiliation: | 1. Department of Chemistry and Center for Molecular Science, Korea Advanced , Institute of Science and Technology , 373-1 Kusung-dong Yusung-gu, Taejon, 305-701, Korea;2. SDI TA TFT CAE group , 575, Shin-Dong, Paldal-Gu, Suwon City, Kyungki-Do, South Korea , 442-395 |
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| Abstract: | Abstract A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close agreement with previous results from both theoretical and experimental studies. The simple idea for controlling the step size according to the Valley Function, provides useful suggestions in searching the global energy minimum structures, and furthermore helps solve the multiple minima problem. |
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| Keywords: | Simulation Monte Carlo Valley Function variable step size global optimization |
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