CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation.
It is well-established that a linear correlation exists between accessible surface areas and experimentally measured solvation energies. Combining this knowledge with an analytic formula for calculation of solvent accessible surfaces, we derive a simple model of desolvation energy as a differentiable function of atomic positions. Additionally, we find that this algorithm is particularly well suited for hardware acceleration on graphics processing units (GPUs), outperforming the CPU by up to two orders of magnitude. We explore the scaling of this desolvation algorithm and provide implementation details applicable to general pairwise algorithms.
Department of Mathematics, University of Wisconsin, Madison, Wisconsin 53706, USA.
David
D
Dynerman
Erick
E
Butzlaff
Julie C
JC
Mitchell
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D008958:Models, Molecular; D012997:Solvents / Q000737:chemistry*; D013499:Surface Properties
D012997:Solvents