Enhanced Van der Waals calculations in genetic algorithms for protein structure prediction

Abstract

SUMMARYSeveral ab initio computational methods for protein structure prediction have been designed using full‐atom models and force field potentials to describe interactions among atoms. Those methods involve the solution of a combinatorial problem with a huge search space. Genetic algorithms (GAs) have shown significant performance increases for such methods. However, even a small protein may require hundreds of thousands of energy function evaluations making GAs suitable only for the prediction of very small proteins. We propose an efficient technique to compute the van der Waals energy (the greatest contributor to protein stability) speeding up the whole GA. First, we developed a Cell‐List Reconstruction procedure that divides the tridimensional space into a cell grid for each new structure that the GA generates. The cells restrict the calculations of van der Waals potentials to ranges in which they are significant, reducing the complexity of such calculations from quadratic to linear. Moreover, the proposal also uses the structure of the cell grid to parallelize the computation of the van der Waals energy, achieving additional speedup. The results have shown a significant reduction in the run time required by a GA. For example, the run time for the prediction of a protein with 147,980 atoms can be reduced from 217 days to 7 h. Copyright © 2012 John Wiley & Sons, Ltd.

Comparing parallel algorithms for van der waals energy with cell-list technique for protein structure prediction

“…This paper compares the results of three parallel paradigms of the celllist: OpenMP version developed in [Bonetti et al 2013], MPI developed in [Bonetti et al 2010b] and the new hybrid parallel implementation of cell-list using MPI and OpenMP concomitantly. All parallel versions reduced the running time of the van der Waals energy calculation, when compared to their sequential version.…”

“…Evdw is the only variable characterized as shared and receives the sum reduction operation. The default number of threads used is equal to the number of available cores [Bonetti et al 2013].…”

Comparing Parallel Algorithms for Van der Waals Energy with Cell-List Technique for Protein Structure Prediction

“…Moreover, flexible parallel techniques applied to cell-list can be used to reduce the run time of the GA. By flexible, we mean the use of distinct parallel programming paradigms in a same algorithm, which, together, can explore diverse benefits available in parallel platforms. This paper compares the results of three cell-list parallel programs: OpenMP version developed in [Bonetti et al 2013], MPI developed in [Bonetti et al 2010] and the new hybrid parallel implementation of cell-list using MPI and OpenMP concomitantly. All parallel versions reduced the running time of the van der Waals energy calculation, when compared to the sequential version.…”

“…In the recent literature, there are different parallel solutions available aiming to minimize the execution time of such algorithms [Benítez and Lopes 2010, Bonetti et al 2010, Bonetti et al 2013. Parallel algorithms in this context usually have distinct and limited performance, mainly because they are specific for one programming model and/or computer architecture.…”

“…Parallel algorithms in this context usually have distinct and limited performance, mainly because they are specific for one programming model and/or computer architecture. In [Bonetti et al 2010] and [Bonetti et al 2013], instead by just making parallel the van der Waals energy from its O(n 2 ) algorithm, the authors first improved the efficiency of the energy using the cell-list algorithm, enabling the complexity reduction to O(n).…”