A gradient‐directed Monte Carlo approach for protein design |
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| Authors: | Xiangqian Hu Hao Hu David N Beratan Weitao Yang |
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| Institution: | Department of Chemistry, French Family Science Center, Duke University, Durham, North Carolina 27708‐0346 |
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| Abstract: | We develop a new global optimization strategy, gradient‐directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 |
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| Keywords: | protein sequence design GDMC LCAP RosettaDesign discrete optimization global optimization |
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