Literature DB >> 20218693

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

Imran S Haque1, Vijay S Pande, W Patrick Walters.   

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.

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Year:  2010        PMID： 20218693      PMCID： PMC2865553          DOI： 10.1021/ci100011z

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN： 1549-9596            Impact factor:   4.956


  10 in total

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Authors:  M D Miller; R P Sheridan; S K Kearsley
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2.  Reoptimization of MDL keys for use in drug discovery.

Authors:  Joseph L Durant; Burton A Leland; Douglas R Henry; James G Nourse
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3.  ZINC--a free database of commercially available compounds for virtual screening.

Authors:  John J Irwin; Brian K Shoichet
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4.  A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction.

Authors:  Thomas S Rush; J Andrew Grant; Lidia Mosyak; Anthony Nicholls
Journal:  J Med Chem       Date:  2005-03-10       Impact factor: 7.446

5.  LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities.

Authors:  David Vidal; Michael Thormann; Miquel Pons
Journal:  J Chem Inf Model       Date:  2005 Mar-Apr       Impact factor: 4.956

6.  Lingos, finite state machines, and fast similarity searching.

Authors:  J Andrew Grant; James A Haigh; Barry T Pickup; Anthony Nicholls; Roger A Sayle
Journal:  J Chem Inf Model       Date:  2006 Sep-Oct       Impact factor: 4.956

7.  Accelerating molecular modeling applications with graphics processors.

Authors:  John E Stone; James C Phillips; Peter L Freddolino; David J Hardy; Leonardo G Trabuco; Klaus Schulten
Journal:  J Comput Chem       Date:  2007-12       Impact factor: 3.376

8.  PAPER--accelerating parallel evaluations of ROCS.

Authors:  Imran S Haque; Vijay S Pande
Journal:  J Comput Chem       Date:  2010-01-15       Impact factor: 3.376

9.  970 million druglike small molecules for virtual screening in the chemical universe database GDB-13.

Authors:  Lorenz C Blum; Jean-Louis Reymond
Journal:  J Am Chem Soc       Date:  2009-07-01       Impact factor: 15.419

10.  Accelerating molecular dynamic simulation on graphics processing units.

Authors:  Mark S Friedrichs; Peter Eastman; Vishal Vaidyanathan; Mike Houston; Scott Legrand; Adam L Beberg; Daniel L Ensign; Christopher M Bruns; Vijay S Pande
Journal:  J Comput Chem       Date:  2009-04-30       Impact factor: 3.376
  10 in total
  11 in total

Review 1.  Methods for Similarity-based Virtual Screening.

Authors:  Thomas G Kristensen; Jesper Nielsen; Christian N S Pedersen
Journal:  Comput Struct Biotechnol J       Date:  2013-03-03       Impact factor: 7.271

2.  Drug discovery using very large numbers of patents: general strategy with extensive use of match and edit operations.

Authors:  Barry Robson; Jin Li; Richard Dettinger; Amanda Peters; Stephen K Boyer
Journal:  J Comput Aided Mol Des       Date:  2011-05-03       Impact factor: 3.686

3.  Error bounds on the SCISSORS approximation method.

Authors:  Imran S Haque; Vijay S Pande
Journal:  J Chem Inf Model       Date:  2011-09-08       Impact factor: 4.956

4.  Anatomy of high-performance 2D similarity calculations.

Authors:  Imran S Haque; Vijay S Pande; W Patrick Walters
Journal:  J Chem Inf Model       Date:  2011-09-07       Impact factor: 4.956

5.  GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening.

Authors:  Xin Yan; Qiong Gu; Feng Lu; Jiabo Li; Jun Xu
Journal:  Mol Divers       Date:  2012-10-19       Impact factor: 2.943

6.  GPU-accelerated Chemical Similarity Assessment for Large Scale Databases.

Authors:  Marco Maggioni; Marco Domenico Santambrogio; Jie Liang
Journal:  Procedia Comput Sci       Date:  2011-05-14

7.  GPU accelerated chemical similarity calculation for compound library comparison.

Authors:  Chao Ma; Lirong Wang; Xiang-Qun Xie
Journal:  J Chem Inf Model       Date:  2011-07-01       Impact factor: 4.956

8.  SCISSORS: practical considerations.

Authors:  Steven M Kearnes; Imran S Haque; Vijay S Pande
Journal:  J Chem Inf Model       Date:  2013-12-16       Impact factor: 4.956

9.  Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

Authors:  Michael A Skinnider; Chris A Dejong; Brian C Franczak; Paul D McNicholas; Nathan A Magarvey
Journal:  J Cheminform       Date:  2017-08-16       Impact factor: 5.514

10.  Accelerating Multiple Compound Comparison Using LINGO-Based Load-Balancing Strategies on Multi-GPUs.

Authors:  Chun-Yuan Lin; Chung-Hung Wang; Che-Lun Hung; Yu-Shiang Lin
Journal:  Int J Genomics       Date:  2015-10-13       Impact factor: 2.326
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