SIML: a fast SIMD algorithm for calculating LINGO chemical similarities on GPUs and CPUs

J Chem Inf Model. 2010 Apr 26;50(4):560-4. doi: 10.1021/ci100011z.

Abstract

LINGOs are a holographic measure of chemical similarity based on text comparison of SMILES strings. We present a new algorithm for calculating LINGO similarities amenable to parallelization on SIMD architectures (such as GPUs and vector units of modern CPUs). We show that it is nearly 3x as fast as existing algorithms on a CPU, and over 80x faster than existing methods when run on a GPU.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Benchmarking
  • Computer Graphics*
  • Computers*
  • Databases, Factual
  • Drug Evaluation, Preclinical / methods*
  • Time Factors