• An Evolutionary Profile Guided Greedy Parallel Replica-Exchange Monte Carlo Search Algorithm for Rapid Convergence in Protein Design

    5 days ago - By IEEE/ACM

    Protein design, also known as the inverse protein folding problem, is the identification of a protein sequence that folds into a target protein structure. Protein design is proved as an NP-hard problem. While researchers are working on designing heuristics with an emphasis on new scoring functions, we propose a replica-exchange Monte Carlo search algorithm that ensures faster convergence using a greedy strategy. Using biological insights, we construct an evolutionary profile to encode the amino acid variability in different positions of the target protein from its structural homologs. The...
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  • A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model

    5 days ago - By IEEE/ACM

    The protein folding problem is an important issue in bioinformatics and biochemical physics. One of the most widely studied models of protein folding is the hydrophobic-polar model introduced by Dill. The PFP in the three-dimensional lattice HP model has been shown to be NP-complete; the proposed algorithms for solving the problem can therefore only find near-optimal energy structures for most long benchmark sequences within acceptable time periods. In this paper, we propose a novel algorithm based on the branch-and-bound approach to solve the PFP in the 3D lattice HP model. For 10...
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