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CUSA and CUDE: GPU-accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation

Authors:
David Dynerman  (University of Wisconsin-Madison)
Erick Butzlaff  (University of Wisconsin-Madison)
Julie C. Mitchell  (University of Wisconsin-Madison)
ACM Student Competition Session
Tuesday,  05:15PM - 07:00PM
Room Rotunda Lobby
Abstract:
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. We will present details of our algorithm and timing results along with applications to biomolecular systems of interest.
   IEEE Computer Society  /  ACM     2 0   Y E A R S   -   U N L E A S H I N G   T H E   P O W E R   O F   H P C