Structure optimization in a three-dimensional off-lattice protein model.

Wenqi Huang; Jingfa Liu

doi:10.1002/bip.20400

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Structure optimization in a three-dimensional off-lattice protein model.

Wenqi Huang·Jingfa Liu

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Abstract

We studied a three-dimensional off-lattice AB model with two species of monomers, hydrophobic (A) and hydrophilic (B), and present two optimization algorithms: face-centered-cubic (FCC)-lattice pruned-enriched-Rosenbluth method (PERM) and subsequent conjugate gradient (PERM++) minimization and heuristic conjugate gradient (HCG) simulation based on "off-trap" strategy. In PERM++, we apply the PERM to the FCC-lattice to produce the initial conformation, and conjugate gradient minimization is then used to reach the minimum energy state. Both algorithms have been tested in the three-dimensional AB model for all sequences with lengths 13 < or = n < or = 55. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we renew the putative ground states energy values.

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Algorithms Computer Simulation Hydrophobic and Hydrophilic Interactions Models, Biological Protein Conformation Protein Folding Proteins Thermodynamics Journal Article Research Support, Non-U.S. Gov't

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Wenqi Huang, Jingfa Liu. 2006-06-05. Structure optimization in a three-dimensional off-lattice protein model.. https://doi.org/10.1002/bip.20400

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