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

Mahmood A Rashid,Ma Hakim Newton,Abdul Sattar,Duc Nghia Pham,Md Tamjidul Hoque,Swakkhar Shatabda

doi:10.1186/1471-2105-14-s2-s16

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.

Highlights

Proteins are essentially sequences of amino acids
Our contributions In this paper, we present a novel spiral search algorithm for ab initio protein structure prediction using HP energy model on three-dimensional (3D) FCC lattice
The results are calculated over 50 different runs with identical settings for each algorithm; duration of each run is presented in last column

Summary

Introduction

Proteins are essentially sequences of amino acids. They adopt specific folded three-dimensional structures to perform specific tasks. Given a protein’s amino acid sequence, the problem is to find a three dimensional structure of the protein such that the total interaction. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3dimensional face-centred-cubic lattice for structure mapping. Our work is based on the ab initio approach that only depends on the amino acid sequence of the target protein. In our simplified protein structure prediction model, we use 3D FCC lattice for conformation mapping, HP energy model for conformation evaluation, and a hydrophobic-core centric local search algorithm (SS-Tabu) for conformation search. 3D FCC lattice, and HP energy model are described below

Objectives

Methods

Results