PubChem3D: Similar conformers

Journal of Cheminformatics

Volumn 3, Issue 1, 2011, Pages

  Bolton, Evan E ^a   Kim, Sunghwan ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959715425     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-3-13     Document Type: Article

References (30)

1. PubChem: integrated platform of small molecules and biological activities. EE Bolton Y Wang PA Thiessen SH Bryant, Annual Reports in Computational Chemistry Elsevier, Ralph AW, David CS, 2008 4 217 241
2. PubChem: a public information system for analyzing bioactivities of small molecules. YL Wang JW Xiao TO Suzek J Zhang JY Wang SH Bryant, Nucleic Acids Res 2009 37 623 W633
3. An overview of the PubChem BioAssay resource. YL Wang E Bolton S Dracheva K Karapetyan BA Shoemaker TO Suzek JY Wang JW Xiao J Zhang SH Bryant, Nucleic Acids Res 2010 38 255 D266
4. Database resources of the National Center for Biotechnology Information. EW Sayers T Barrett DA Benson E Bolton SH Bryant K Canese V Chetvernin DM Church M DiCuccio S Federhen,, et al. Nucleic Acids Res 2010 38 5 D16
5. Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings. JD Holliday CY Hu P Willett, Comb Chem High Throughput Screen 2002 5 155 166 (Pubitemid 34475167)
6. Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients. X Chen CH Reynolds, J Chem Inf Comput Sci 2002 42 1407 1414 (Pubitemid 35468329)
7. Analysis and display of the size dependence of chemical similarity coefficients. JD Holliday N Salim M Whittle P Willett, J Chem Inf Comput Sci 2003 43 819 828
8. PubChem substructure fingerprint description. ftp://ftp.ncbi.nlm.nih.gov/ pubchem/specifications/pubchem-fingerprints.pdf
9. A gaussian description of molecular shape. JA Grant BT Pickup, J Phys Chem 1995 99 3503 3510
10. ROCS - Rapid Overlay of Chemical Structures. Version 2.2, OpenEye Scientific Software, Inc.: Santa Fe, NM 2006
11. PAPERaccelerating parallel evaluations of ROCS. IS Haque VS Pande, J Comput Chem 2010 31 117 132
12. ShapeTK-C++. Version 1.8.0, OpenEye Scientific Software, Inc.: Santa Fe, NM 2010
13. Small molecule shape-fingerprints. JA Haigh BT Pickup JA Grant A Nicholls, J Chem Inf Model 2005 45 673 684 (Pubitemid 40795171)
14. Fast 3D shape screening of large chemical databases through alignment-recycling. F Fontaine E Bolton Y Borodina SH Bryant, Chem Cent J 2007 1 12
15. PubChem3D: diversity of shape. EE Bolton S Kim SH Bryant, J Cheminformatics 2011 3 9
16. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. TS Rush JA Grant L Mosyak A Nicholls, J Med Chem 2005 48 1489 1495 (Pubitemid 40364556)
17. A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape. JA Grant MA Gallardo BT Pickup, J Comput Chem 1996 17 1653 1666 (Pubitemid 126535414)
18. Medical Subject Headings. http://www.ncbi.nlm.nih.gov/mesh
19. PubMed. http://www.pubmed.gov
20. MMDB: annotating protein sequences with Entrez's 3D-structure database. Y Wang KJ Addess J Chen LY Geer J He S He S Lu T Madej A Marchler-Bauer PA Thiessen,, et al. Nucleic Acids Res 2007 35 298 D300
21. DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. C Knox V Law T Jewison P Liu S Ly A Frolkis A Pon K Banco C Mak V Neveu,, et al. Nucleic Acids Res 2011 39 1035 D1041
22. Zomepirac. DC McLeod, Drug Intelligence & Clinical Pharmacy 1981 15 522 530
23. Pharmacologic properties of fenbufen. SS Kerwar, Am J Med 1983 75 62 69 (Pubitemid 14230802)
24. Inhibition of prostaglandin activity and synthesis by fenbufen (a new nonsteroidal antiinflammatory agent) and one of its metabolites. EL Tolman JE Birnbaum FS Chiccarelli J Panagides AE Sloboda, Advances in Prostaglandin and Thromboxane Research 1976 1 133 138
25. Pharmacology of benoxaprofen (2-[4-chlorophenyl] - methyl-5-benzoxazole acetic acid), LRCL 3794, a new compound with anti-inflammatory activity apparently unrelated to inhibition of prostaglandin synthesis. CH Cashin W Dawson EA Kitchen, J Pharm Pharmacol 1977 29 330 336 (Pubitemid 8113548)
26. Molecular shape and medicinal chemistry: a perspective. A Nicholls GB McGaughey RP Sheridan AC Good G Warren M Mathieu SW Muchmore SP Brown JA Grant JA Haigh,, et al. J Med Chem 2010 53 3862 3886
27. Application of belief theory to similarity data fusion for use in analog searching and lead hopping. SW Muchmore DA Debe JT Metz SP Brown YC Martin PJ Hajduk, J Chem Inf Model 2008 48 941 948
28. PubChem3D: conformer generation. EE Bolton S Kim SH Bryant, J Cheminformatics 2011 3 4
29. van der Waals volumes and radii. A Bondi, J Phys Chem 1964 68 441 451
30. Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. JEJ Mills PM Dean, J Comput Aid Mol Des 1996 10 607 622 (Pubitemid 126712453)