title: Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction.
abstract: Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this problem. For protein structure modeling, an off-lattice model provides limited scopes to exercise and evaluate the algorithmic developments due to its astronomically large set of data-points. In contrast, an on-lattice model widens the scopes and permits studying the relatively larger proteins because of its finite set of data-points. In this work, we took the full advantage of an on-lattice model by using a face-centered-cube lattice that has the highest packing density with the maximum degree of freedom. We proposed a graded energy-strategically mixes the Miyazawa-Jernigan (MJ) energy with the hydrophobic-polar (HP) energy-based genetic algorithm (GA) for conformational search. In our application, we introduced a 2 × 2 HP energy guided macro-mutation operator within the GA to explore the best possible local changes exhaustively. Conversely, the 20 × 20 MJ energy model-the ultimate objective function of our GA that needs to be minimized-considers the impacts amongst the 20 different amino acids and allow searching the globally acceptable conformations. On a set of benchmark proteins, our proposed approach outperformed state-of-the-art approaches in terms of the free energy levels and the root-mean-square deviations.
authors.affiliation: SCIMS, University of the South Pacific, Laucala Bay, Suva, Fiji; IIIS, Griffith University, Brisbane, QLD, Australia. Electronic address: mahmood.rashid@usp.ac.fj.
authors.forename: Mahmood A
authors.initials: MA
authors.lastname: Rashid
authors.affiliation: CS, University of New Orleans, LA, USA. Electronic address: siqbal1@uno.edu.
authors.forename: Sumaiya
authors.initials: S
authors.lastname: Iqbal
authors.affiliation: CIS, University of Massachusetts Dartmouth, MA, USA. Electronic address: fkhatib@umassd.edu.
authors.forename: Firas
authors.initials: F
authors.lastname: Khatib
authors.affiliation: CS, University of New Orleans, LA, USA. Electronic address: thoque@uno.edu.
authors.forename: Md Tamjidul
authors.initials: MT
authors.lastname: Hoque
authors.affiliation: IIIS, Griffith University, Brisbane, QLD, Australia. Electronic address: a.sattar@griffith.edu.au.
authors.forename: Abdul
authors.initials: A
authors.lastname: Sattar
mesh_terms: D000465:Algorithms; D008962:Models, Theoretical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: Ab initio protein structure prediction; FCC lattice; Genetic algorithms; Hydrophobic-polar model; Miyazawa–Jernigan model