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Graduate Category: Engineering and Technology Degree Level: PhD Abstract ID#1405 Novel Parallel Approach for Protein Coordinate Conversion Mahsa Bayati [email protected] Advisors: Miriam Leeser, Jaydeep P.Bardhan [email protected],[email protected] Abstract • Converting internal coordinates of atomic structure to Cartesian is time consuming • Important application: Protein Engineering Fitting atomic structure to experimental data Protein Coordinates Large protein complexes ● ● All current methods are serial because of the dependent structure of proteins Ours is the first parallel solution for this problem Parallel Reduction-based Algorithm of Reverse Conversion moves in time ● millions of atoms Titin (muscle protein) : 539022 atoms ● Naïve algorithm Our solution Merge and reduce local coordinate spaces No dependency Find local coordinates Part of the structure of titin Time complexity Two methods to specify atoms’ positions Reverse Cartesian Forward Internal n residues Naïve reduction R : denotes the side chain Internal Coordinates Bond length Calculate transformation matrices Bond angle Our method Dihedral angle Backbone of amino acid 4 non-hydrogen atoms per atoms Serially walking over the dependent structure Time complexity Apply transformation matrices to compute global Cartesian Coordinates independently n residues 10-18x end-to-end speedup and good scalability Reverse Conversion Results CPU: Intel Xeon E2620 Sandy Bridge ● GPU: NVIDIA Tesla K-20m (Kepler) ● Architecture Test Cases ● Lactate DeHdrogenase (LDH) contains 8 chains of protein ● Chain of alanine to show scalability Future work ● Cycles disulphide bond proline ● Side chain ● Large protein Acknowledgements Mahsa Bayati and Miriam Leeser are supported in part by NSF award number CCF-1218075 Jaydeep P. Bardhan is supported in part by NIH award number R21GM102642.
