A GPU based Conformational Entropy Calculation Method

Conformational entropy calculation, usually computed by normal mode analysis (NMA), is a time-consuming step in MM-PB/GBSA calculations. Here, instead of NMA, a solvent accessible surface area (SAS) based model was employed to compute the conformational entropy. A new fast GPU-based method called MURCIA (Molecular Unburied Rapid Calculation of Individual Areas) was used instead of the traditional Shrake-Rupley algorithm to accelerate the calculation of SASA for each atom. MURCIA employs two different kernels to determine each atom’s neighbors. First one (K1) uses just brute force for the calculation of atomic neighbours, while the second one (K2) uses an advanced algorithm involving hardware interpolations via GPU texture memory unit for such purpose. These two kernels have their own advantages depending on the protein size. The algorithm is extensively evaluated in three protein datasets, and achieves good results for all of them, being this method around two orders of magnitude faster than the former algorithm at the size of 10. Finally, further improvements of the algorithm are discussed. IWBBIO 2013. Proceedings Granada, 18-20 March, 2013 735