PubChem3D: Conformer generation
10.1186/1758-2946-3-4
Crossref journal-article
Springer Science and Business Media LLC
Journal of Cheminformatics (297)
Bibliography

Bolton, E. E., Kim, S., & Bryant, S. H. (2011). PubChem3D: Conformer generation. Journal of Cheminformatics, 3(1).

Authors 3
  1. Evan E Bolton (first)
  2. Sunghwan Kim (additional)
  3. Stephen H Bryant (additional)
References 33 Referenced 38
  1. Wang YL, Xiao JW, Suzek TO, Zhang J, Wang JY, Bryant SH: PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 2009, 37: W623-W633. 10.1093/nar/gkp456. (10.1093/nar/gkp456) / Nucleic Acids Res by YL Wang (2009)
  2. Wang YL, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang JY, Xiao JW, Zhang J, Bryant SH: An overview of the PubChem BioAssay resource. Nucleic Acids Res. 2010, 38: D255-D266. 10.1093/nar/gkp965. (10.1093/nar/gkp965) / Nucleic Acids Res by YL Wang (2010)
  3. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010, 38: D5-D16. 10.1093/nar/gkp967. (10.1093/nar/gkp967) / Nucleic Acids Res by EW Sayers (2010)
  4. Bolton EE, Wang Y, Thiessen PA, Bryant SH: PubChem: integrated platform of small molecules and biological activities. Annual Reports in Computational Chemistry. Edited by: Ralph AW. 2008, David CS: Elsevier, 4: 217-241. 10.1016/S1574-1400(08)00012-1. / Annual Reports in Computational Chemistry by EE Bolton (2008)
  5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000, 28: 235-242. 10.1093/nar/28.1.235. (10.1093/nar/28.1.235) / Nucleic Acids Res by HM Berman (2000)
  6. Bostrom J: Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. Journal of Computer-Aided Molecular Design. 2001, 15: 1137-1152. 10.1023/A:1015930826903. (10.1023/A:1015930826903) / Journal of Computer-Aided Molecular Design by J Bostrom (2001)
  7. Nicklaus MC, Wang SM, Driscoll JS, Milne GWA: Conformational changes of small molecules binding to proteins. Bioorganic & Medicinal Chemistry. 1995, 3: 411-428. 10.1016/0968-0896(95)00031-B. (10.1016/0968-0896(95)00031-B) / Bioorganic & Medicinal Chemistry by MC Nicklaus (1995)
  8. Nissink JWM, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R: A new test set for validating predictions of protein-ligand interaction. Proteins-Structure Function and Genetics. 2002, 49: 457-471. 10.1002/prot.10232. (10.1002/prot.10232) / Proteins-Structure Function and Genetics by JWM Nissink (2002)
  9. Westbrook J, Feng ZK, Burkhardt K, Berman HM: Validation of protein structures for Protein Data Bank. Macromolecular Crystallography, Pt D. 2003, San Diego: Academic Press Inc, 374: 370-385. full_text. Methods in Enzymology, (10.1016/S0076-6879(03)74017-8) / Macromolecular Crystallography, Pt D by J Westbrook (2003)
  10. Acharya KR, Lloyd MD: The advantages and limitations of protein crystal structures. Trends Pharmacol Sci. 2005, 26: 10-14. 10.1016/j.tips.2004.10.011. (10.1016/j.tips.2004.10.011) / Trends Pharmacol Sci by KR Acharya (2005)
  11. Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT: Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. Journal of Chemical Information and Modeling. 2010, 50: 572-584. 10.1021/ci100031x. (10.1021/ci100031x) / Journal of Chemical Information and Modeling by PCD Hawkins (2010)
  12. Murrall NW, Davies EK: Conformational freedom in 3-D databases. 1. Techniques. J Chem Inf Comput Sci. 1990, 30: 312-316. (10.1021/ci00067a016) / J Chem Inf Comput Sci by NW Murrall (1990)
  13. Hurst T: Flexible 3D searching: the directed tweak technique. J Chem Inf Comput Sci. 1994, 34: 190-196. (10.1021/ci00017a025) / J Chem Inf Comput Sci by T Hurst (1994)
  14. Klebe G, Mietzner T: A fast and efficient method to generate biologically relevant conformations. Journal of Computer-Aided Molecular Design. 1994, 8: 583-606. 10.1007/BF00123667. (10.1007/BF00123667) / Journal of Computer-Aided Molecular Design by G Klebe (1994)
  15. Renner S, Schwab CH, Gasteiger J, Schneider G: Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors. J Chem Inf Model. 2006, 46: 2324-2332. 10.1021/ci050075s. (10.1021/ci050075s) / J Chem Inf Model by S Renner (2006)
  16. Greene J, Kahn S, Savoj H, Sprague P, Teig S: Chemical function queries for 3D database search. J Chem Inf Comput Sci. 1994, 34: 1297-1308. (10.1021/ci00022a012) / J Chem Inf Comput Sci by J Greene (1994)
  17. Kirchmair J, Wolber G, Laggner C, Langer T: Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations. J Chem Inf Model. 2006, 46: 1848-1861. 10.1021/ci060084g. (10.1021/ci060084g) / J Chem Inf Model by J Kirchmair (2006)
  18. Bostrom J, Greenwood JR, Gottfries J: Assessing the performance of OMEGA with respect to retrieving bioactive conformations. Journal of Molecular Graphics & Modelling. 2003, 21: 449-462. 10.1016/S1093-3263(02)00204-8. (10.1016/S1093-3263(02)00204-8) / Journal of Molecular Graphics & Modelling by J Bostrom (2003)
  19. OMEGA. 2006, Version 2.1, OpenEye Scientific Software, Inc.: Santa Fe, NM
  20. Borodina YV, Bolton E, Fontaine F, Bryant SH: Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. J Chem Inf Model. 2007, 47: 1428-1437. 10.1021/ci7000956. (10.1021/ci7000956) / J Chem Inf Model by YV Borodina (2007)
  21. Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, et al: MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 2003, 31: 474-477. 10.1093/nar/gkg086. (10.1093/nar/gkg086) / Nucleic Acids Res by J Chen (2003)
  22. Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, et al: MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res. 2007, 35: D298-D300. 10.1093/nar/gkl952. (10.1093/nar/gkl952) / Nucleic Acids Res by Y Wang (2007)
  23. OpenEye Omega Toolkit - C++. [http://www.eyesopen.com]
  24. ROCS - Rapid Overlay of Chemical Structures. 2006, Version 2.2, OpenEye Scientific Software, Inc.: Santa Fe, NM
  25. 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. 10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K. (10.1002/(SICI)1096-987X(19961115)17:14<1653::AID-JCC7>3.0.CO;2-K) / J Comput Chem by JA Grant (1996)
  26. 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. 10.1021/jm040163o. (10.1021/jm040163o) / J Med Chem by TS Rush (2005)
  27. Halgren TA: Merck molecular force field. 1. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem. 1996, 17: 490-519. 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P. (10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P) / J Comput Chem by TA Halgren (1996)
  28. Halgren TA: Merck molecular force field. 2. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J Comput Chem. 1996, 17: 520-552. 10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W. (10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W) / J Comput Chem by TA Halgren (1996)
  29. Halgren TA: Merck molecular force field. 3. Molecular geometries and vibrational frequencies for MMFF94. J Comput Chem. 1996, 17: 553-586. 10.1002/(SICI)1096-987X(199604)17:5/6<553::AID-JCC3>3.0.CO;2-T. (10.1002/(SICI)1096-987X(199604)17:5/6<553::AID-JCC3>3.0.CO;2-T) / J Comput Chem by TA Halgren (1996)
  30. Halgren TA, Nachbar RB: Merck molecular force field. 4. Conformational energies and geometries for MMFF94. J Comput Chem. 1996, 17: 587-615. / J Comput Chem by TA Halgren (1996)
  31. Halgren TA: Merck molecular force field. 5. Extension of MMFF94 using experimental data, additional computational data, and empirical rules. J Comput Chem. 1996, 17: 616-641. 10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X. (10.1002/(SICI)1096-987X(199604)17:5/6<616::AID-JCC5>3.0.CO;2-X) / J Comput Chem by TA Halgren (1996)
  32. Halgren TA: MMFF VI. MMFF94s option for energy minimization studies. J Comput Chem. 1999, 20: 720-729. 10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X. (10.1002/(SICI)1096-987X(199905)20:7<720::AID-JCC7>3.0.CO;2-X) / J Comput Chem by TA Halgren (1999)
  33. Halgren TA: MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. J Comput Chem. 1999, 20: 730-748. 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T. (10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T) / J Comput Chem by TA Halgren (1999)
Dates
Type When
Created 14 years, 6 months ago (Feb. 8, 2011, 9:49 a.m.)
Deposited 3 years, 11 months ago (Sept. 1, 2021, 8:17 a.m.)
Indexed 1 year, 2 months ago (June 14, 2024, 1:50 p.m.)
Issued 14 years, 6 months ago (Jan. 27, 2011)
Published 14 years, 6 months ago (Jan. 27, 2011)
Published Online 14 years, 6 months ago (Jan. 27, 2011)
Published Print 13 years, 8 months ago (Dec. 1, 2011)
Funders 0

None

@article{Bolton_2011, title={PubChem3D: Conformer generation}, volume={3}, ISSN={1758-2946}, url={http://dx.doi.org/10.1186/1758-2946-3-4}, DOI={10.1186/1758-2946-3-4}, number={1}, journal={Journal of Cheminformatics}, publisher={Springer Science and Business Media LLC}, author={Bolton, Evan E and Kim, Sunghwan and Bryant, Stephen H}, year={2011}, month=jan }