Structure optimization in a three-dimensional off-lattice protein model
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Updated: Jul 31, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
1School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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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