Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice

Abstract

BackgroundProtein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3-dimensional face-centred-cubic lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (H-core) is essential for the progress of the search. The H-core helps find a stable structure with the lowest possible free energy.ResultsIn order to build H-cores, we present a new Spiral Search algorithm based on tabu-guided local search. Our algorithm uses a novel H-core directed guidance heuristic that squeezes the structure around a dynamic hydrophobic-core centre. We applied random walks to break premature H-cores and thus to avoid early convergence. We also used a novel relay-restart technique to handle stagnation.ConclusionsWe have tested our algorithms on a set of benchmark protein sequences. The experimental results show that our spiral search algorithm outperforms the state-of-the-art local search algorithms for simplified protein structure prediction. We also experimentally show the effectiveness of the relay-restart.

Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction

“…if mutation( ) then (10) foreach ∈ do (11) newP.add(mutConf( )) (12) else (13) while ¬ full( ) do (14) , ← randomConfs(…”

Soft Computing Techniques for the Protein Folding Problem on High Performance Computing Architectures

“…Results show to be promising and reliable for proteins consisting in less than 100 aminoacids. Eventually, all the previous results on HP energy models on 3D FCC lattices have been outperformed by the work in [200]. This paper defines a hydrophobic-core centric local search algorithm named SS-Tabu.…”

Exact methods for lattice protein models

“…This so-called hydrophobic core is present in almost all globular water-solved protein structures. It is central to the CPSP approach and was also used in recent local search methods [22,34]. Beneath the suggested energy potentials by Dill and co-workers [58] (e(S i , S j ) = -1, if S i and S j are hydrophobic; 0, otherwise), other potentials have been applied [47,59].…”

“…As exhaustive structure enumeration approaches [20] are restricted to very short sequence lengths, usually heuristic methods are applied. They apply various techniques, e.g., simulated annealing [21,22], quantum annealing [23], ant colonization optimization [24], evolutionary algorithms [25], energy landscape paving [26], large neighborhood search [27,28], constraint programming [29][30][31], or dedicated search heuristics [32][33][34][35]. They enable performance-guaranteed approximations close to the optimum for both backbone-only [36,37] and sidechain models [38,39].…”