Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Apr 26;50(4):560-4.
doi: 10.1021/ci100011z.

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

Imran S Haque  1 , Vijay S Pande, W Patrick Walters
Affiliations

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

Imran S Haque et al. J Chem Inf Model. .

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.

PubMed Disclaimer

Figures

Algorithm 1
Algorithm 1
Sparse-vector algorithm to calculate LINGO Tanimoto between two molecules in sorted multiset representation
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Nikolova N, Jaworska J. Approaches to Measure Chemical Similarity - a Review. QSAR & Combin Sci. 2003;22:1006–1026.
    1. Grant JA, Gallardo MA, Pickup BT. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape. J Comput Chem. 1996;17:1653–1666.
    1. Miller MD, Sheridan RP, Kearsley SK. SQ: A Program for Rapidly Producing Phar-macophorically Relevent Molecular Superpositions. J Med Chem. 1999;42:1505–1514. - PubMed
    1. Rush TS, Grant JA, Mosyak L, Nicholls A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem. 2005;48:1489–1495. - PubMed
    1. Carhart RE, Smith DH, Venkataraghavan R. Atom pairs as molecular features in structure-activity studies: definition and applications. J Chem Inf Comput Sci. 1985;25:64–73.

Publication types