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Items: 17

1.

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database.

Hawkins PC, Skillman AG, Warren GL, Ellingson BA, Stahl MT.

J Chem Inf Model. 2010 Apr 26;50(4):572-84. doi: 10.1021/ci100031x.

2.

An overview of the PubChem BioAssay resource.

Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang J, Xiao J, Zhang J, Bryant SH.

Nucleic Acids Res. 2010 Jan;38(Database issue):D255-66. doi: 10.1093/nar/gkp965. Epub 2009 Nov 19.

3.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16. doi: 10.1093/nar/gkp967. Epub 2009 Nov 12.

4.

PubChem: a public information system for analyzing bioactivities of small molecules.

Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W623-33. doi: 10.1093/nar/gkp456. Epub 2009 Jun 4.

5.

Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space.

Borodina YV, Bolton E, Fontaine F, Bryant SH.

J Chem Inf Model. 2007 Jul-Aug;47(4):1428-37. Epub 2007 Jun 15.

6.

MMDB: annotating protein sequences with Entrez's 3D-structure database.

Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, Zhang N, Bryant SH.

Nucleic Acids Res. 2007 Jan;35(Database issue):D298-300. Epub 2006 Nov 29.

7.

Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors.

Renner S, Schwab CH, Gasteiger J, Schneider G.

J Chem Inf Model. 2006 Nov-Dec;46(6):2324-32.

PMID:
17125176
8.
9.

A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction.

Rush TS 3rd, Grant JA, Mosyak L, Nicholls A.

J Med Chem. 2005 Mar 10;48(5):1489-95.

PMID:
15743191
10.

The advantages and limitations of protein crystal structures.

Acharya KR, Lloyd MD.

Trends Pharmacol Sci. 2005 Jan;26(1):10-4. Review.

PMID:
15629199
11.

Assessing the performance of OMEGA with respect to retrieving bioactive conformations.

Boström J, Greenwood JR, Gottfries J.

J Mol Graph Model. 2003 Mar;21(5):449-62.

PMID:
12543140
12.

MMDB: Entrez's 3D-structure database.

Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH.

Nucleic Acids Res. 2003 Jan 1;31(1):474-7.

13.

A new test set for validating predictions of protein-ligand interaction.

Nissink JW, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R.

Proteins. 2002 Dec 1;49(4):457-71.

PMID:
12402356
14.
15.

The Protein Data Bank.

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE.

Nucleic Acids Res. 2000 Jan 1;28(1):235-42.

16.

Conformational changes of small molecules binding to proteins.

Nicklaus MC, Wang S, Driscoll JS, Milne GW.

Bioorg Med Chem. 1995 Apr;3(4):411-28.

PMID:
8581425
17.

A fast and efficient method to generate biologically relevant conformations.

Klebe G, Mietzner T.

J Comput Aided Mol Des. 1994 Oct;8(5):583-606.

PMID:
7876902

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