A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 18; no. 2; pp. 455 - 462
• Main Authors: Chou, Hsin-Hung, Hsu, Ching-Tien, Chen, Li-Hsuan, Lin, Yue-Cheng, Hsieh, Sun-Yuan
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.03.2021; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: 3D HP model; 3D-NBB algorithm; Algorithms; Amino acids; Benchmarks; Bioinformatics; Biological system modeling; Branch-and-Bound algorithm; Computational Biology - methods; Computational modeling; Folding; Hydrophobicity; Lattices; Models, Molecular; Protein Conformation; Protein Folding; Protein folding problem; Protein structure prediction problem; Proteins; Proteins - chemistry; Proteins - metabolism; Solid modeling; Three dimensional models; Three-dimensional displays
• ISSN: 1545-5963; 1557-9964; 1557-9964
• DOI: 10.1109/TCBB.2019.2934102

The protein folding problem (PFP) is an important issue in bioinformatics and biochemical physics. One of the most widely studied models of protein folding is the hydrophobic-polar (HP) model introduced by Dill. The PFP in the three-dimensional (3D) 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 48-monomer benchmark sequences, our proposed algorithm finds the lowest energies so far within comparable computation times than previous methods.