A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing

• Published in: Mathematical and computational applications 2021-06, Vol.26 (2), p.39
• Main Authors: Sánchez-Hernández, Juan P., Frausto-Solís, Juan, González-Barbosa, Juan J., Soto-Monterrubio, Diego A., Maldonado-Nava, Fanny G., Castilla-Valdez, Guadalupe
• Format: Article
• Language: English
• Subjects: Algorithms; Amino acids; Energy; Hybrid Simulated Annealing; Methodology; Methods; Metropolis; Optimization; Peptides; Protein folding; protein structure prediction; Proteins; Simulated annealing; Simulation; structural biology; Template-Based Modeling
• ISSN: 2297-8747; 1300-686X; 2297-8747
• DOI: 10.3390/mca26020039

The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.