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

Journal of Chemical Information and Modeling

Volumn 50, Issue 4, 2010, Pages 560-564

  Haque, Imran S ^a   Pande, Vijay S ^a,b   Walters, W Patrick ^c  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

^c VERTEX PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

CHEMICAL SIMILARITY; PARALLELIZATIONS; SIMD ARCHITECTURE; VECTOR UNITS;

PROGRAM PROCESSORS;

ALGORITHM; ARTICLE; COMPUTER; COMPUTER GRAPHICS; DRUG SCREENING; FACTUAL DATABASE; METHODOLOGY; QUALITY CONTROL; TIME;

ALGORITHMS; BENCHMARKING; COMPUTER GRAPHICS; COMPUTERS; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL; TIME FACTORS;

EID: 77952004390     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100011z     Document Type: Article

References (15)

1. Nikolova, N.; Jaworska, J. Approaches to Measure Chemical Similarity-A Review QSAR Comb. Sci. 2003, 22, 1006-1026
2. Grant, J. A.; Gallardo, M. A.; Pickup, B. T. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape J. Comput. Chem. 1996, 17, 1653-1666
3. Miller, M. D.; Sheridan, R. P.; Kearsley, S. K. SQ: A Program for Rapidly Producing Pharmacophorically Relevent Molecular Superpositions J. Med. Chem. 1999, 42, 1505-1514
4. Rush, T. S.; Grant, J. A.; 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
5. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs As Molecular Features in Structure-Activity Studies: Definition and Applications J. Chem. Inf. Comput. Sci. 1985, 25, 64-73
6. Durant, J. L.; Leland, B. A.; Henry, D. R.; Nourse, J. G. Reoptimization of MDL Keys for Use in Drug Discovery J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280
7. Vidal, D.; Thormann, M.; Pons, M. LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities J. Chem. Inf. Model 2005, 45, 386-393
8. Grant, J. A.; Haigh, J. A.; Pickup, B. T.; Nicholls, A.; Sayle, R. A. Lingos, Finite State Machines, and Fast Similarity Searching J. Chem. Inf. Model. 2006, 46, 1912-1918
9. Irwin, J. J.; Shoichet, B. K. ZINC-A Free Database of Commercially Available Compounds for Virtual Screening J. Chem. Inf. Model. 2005, 45, 177-182
10. Blum, L. C.; Reymond, J.-L. 970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13 J. Am. Chem. Soc. 2009, 131, 8732-8733
11. Butina, D. Unsupervised Data Base Clustering Based on Daylights Fingerprint and Tanimoto Similarity: A Fast and Automated Way To Cluster Small and Large Data Sets J. Chem. Inf. Comput. Sci. 1999, 39, 747-750
12. Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. Accelerating Molecular Dynamic Simulation on Graphics Processing Units J. Comput. Chem. 2009, 30, 864-872
13. Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K. Accelerating Molecular Modeling Applications with Graphics Processors J. Comput. Chem. 2007, 28, 2618-2640
14. Haque, I. S.; Pande, V. S. PAPER-Accelerating Parallel Evaluations of ROCS J. Comput. Chem. 2009, 31, 117-132
15. Kloeckner, A.; Pinto, N.; Lee, Y.; Catanzaro, B.; Ivanov, P.; Fasih, A. PyCUDA: GPU Run-Time Code Generation for High-Performance Computing. arXiv:0911.3456v1 [cs.DC].