Accelerated Structural Bioinformatics for Drug Discovery

Document Type

Article

Publication Date

7-23-2015

Abstract

This chapter documents the parallelization of, eFindSite, a ligand binding site prediction software used in drug discovery and design. eFindSite is a complex hybrid C++/Fortran77 code, which includes significant legacy Fortran software that was not thread-safe, to utilize parallelism and obtain a 17.6× speedup. Solutions to challenges in moving this code to parallelism serve as lessons with wide applicability and are examined in detail. Porting extensive use of thread-unsafe common blocks in the Fortran77 code using OpenMP to make thread-private copies is discussed. With minimal modifications, it is demonstrated how modern drug discovery can be accelerated by parallel systems.

Publication Source (Journal or Book title)

High Performance Parallelism Pearls Multicore and Many Core Programming Approaches

First Page

55

Last Page

72

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