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Results: 1 to 20 of 186

1.

Pathway analysis for drug repositioning based on public database mining.

Pan Y, Cheng T, Wang Y, Bryant SH.

J Chem Inf Model. 2014 Feb 24;54(2):407-18. doi: 10.1021/ci4005354. Epub 2014 Feb 5.

PMID:
24460210
[PubMed - in process]
2.

An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data.

Hao M, Wang Y, Bryant SH.

Anal Chim Acta. 2014 Jan 2;806:117-27. doi: 10.1016/j.aca.2013.10.050. Epub 2013 Nov 6.

PMID:
24331047
[PubMed - indexed for MEDLINE]
3.

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D297-303. doi: 10.1093/nar/gkt1208. Epub 2013 Dec 6.

PMID:
24319143
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

PubChem BioAssay: 2014 update.

Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1075-82. doi: 10.1093/nar/gkt978. Epub 2013 Nov 5.

PMID:
24198245
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Characterizing protein domain associations by Small-molecule ligand binding.

Li Q, Cheng T, Wang Y, Bryant SH.

J Proteome Sci Comput Biol. 2012 Dec 3;1. pii: 6.

PMID:
23745168
[PubMed]
Free PMC Article
6.

Pharmacophore and 3D-QSAR characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) inhibitors.

Pan Y, Wang Y, Bryant SH.

J Chem Inf Model. 2013 Apr 22;53(4):938-47. doi: 10.1021/ci300625c. Epub 2013 Apr 4.

PMID:
23496085
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

PubChem3D: conformer ensemble accuracy.

Kim S, Bolton EE, Bryant SH.

J Cheminform. 2013 Jan 7;5(1):1. doi: 10.1186/1758-2946-5-1.

PMID:
23289532
[PubMed]
Free PMC Article
8.

CDD: conserved domains and protein three-dimensional structure.

Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D348-52. doi: 10.1093/nar/gks1243. Epub 2012 Nov 28.

PMID:
23197659
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis.

Kim S, Bolton EE, Bryant SH.

J Cheminform. 2012 Nov 7;4(1):28. doi: 10.1186/1758-2946-4-28.

PMID:
23134593
[PubMed]
Free PMC Article
10.

FSelector: a Ruby gem for feature selection.

Cheng T, Wang Y, Bryant SH.

Bioinformatics. 2012 Nov 1;28(21):2851-2. doi: 10.1093/bioinformatics/bts528. Epub 2012 Aug 31.

PMID:
22942017
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Annotation of functional sites with the Conserved Domain Database.

Derbyshire MK, Lanczycki CJ, Bryant SH, Marchler-Bauer A.

Database (Oxford). 2012 Mar 20;2012:bar058. doi: 10.1093/database/bar058. Print 2012.

PMID:
22434827
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge.

Sridhara V, Bai DL, Chi A, Shabanowitz J, Hunt DF, Bryant SH, Geer LY.

Proteome Sci. 2012 Feb 9;10(1):8. doi: 10.1186/1477-5956-10-8.

PMID:
22321509
[PubMed]
Free PMC Article
13.

Homology inference of protein-protein interactions via conserved binding sites.

Tyagi M, Thangudu RR, Zhang D, Bryant SH, Madej T, Panchenko AR.

PLoS One. 2012;7(1):e28896. doi: 10.1371/journal.pone.0028896. Epub 2012 Jan 31.

PMID:
22303436
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Structure-based virtual screening for drug discovery: a problem-centric review.

Cheng T, Li Q, Zhou Z, Wang Y, Bryant SH.

AAPS J. 2012 Mar;14(1):133-41. doi: 10.1208/s12248-012-9322-0. Epub 2012 Jan 27. Review.

PMID:
22281989
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Modulating protein-protein interactions with small molecules: the importance of binding hotspots.

Thangudu RR, Bryant SH, Panchenko AR, Madej T.

J Mol Biol. 2012 Jan 13;415(2):443-53. doi: 10.1016/j.jmb.2011.12.026. Epub 2011 Dec 16.

PMID:
22198293
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

PubChem's BioAssay Database.

Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA, Bolton E, Gindulyte A, Bryant SH.

Nucleic Acids Res. 2012 Jan;40(Database issue):D400-12. doi: 10.1093/nar/gkr1132. Epub 2011 Dec 2.

PMID:
22140110
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25. doi: 10.1093/nar/gkr1184. Epub 2011 Dec 2.

PMID:
22140104
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MMDB: 3D structures and macromolecular interactions.

Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH.

Nucleic Acids Res. 2012 Jan;40(Database issue):D461-4. doi: 10.1093/nar/gkr1162. Epub 2011 Dec 1.

PMID:
22135289
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Automated annotation of chemical names in the literature with tunable accuracy.

Zhang JD, Geer LY, Bolton EE, Bryant SH.

J Cheminform. 2011 Nov 22;3(1):52. doi: 10.1186/1758-2946-3-52.

PMID:
22107874
[PubMed]
Free PMC Article
20.

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.

Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D834-40. doi: 10.1093/nar/gkr997. Epub 2011 Nov 18.

PMID:
22102591
[PubMed - indexed for MEDLINE]
Free PMC Article

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