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Items: 37

1.

PubChem 2019 update: improved access to chemical data.

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1102-D1109. doi: 10.1093/nar/gky1033.

2.

Finding Potential Multitarget Ligands Using PubChem.

Kim S, Shoemaker BA, Bolton EE, Bryant SH.

Methods Mol Biol. 2018;1825:63-91. doi: 10.1007/978-1-4939-8639-2_2.

PMID:
30334203
3.

Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows.

Goncearenco A, Li M, Simonetti FL, Shoemaker BA, Panchenko AR.

Methods Mol Biol. 2017;1647:221-236. doi: 10.1007/978-1-4939-7201-2_15.

4.

PubChem BioAssay: 2017 update.

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

Nucleic Acids Res. 2017 Jan 4;45(D1):D955-D963. doi: 10.1093/nar/gkw1118. Epub 2016 Nov 29.

5.

Literature information in PubChem: associations between PubChem records and scientific articles.

Kim S, Thiessen PA, Cheng T, Yu B, Shoemaker BA, Wang J, Bolton EE, Wang Y, Bryant SH.

J Cheminform. 2016 Jun 10;8:32. doi: 10.1186/s13321-016-0142-6. eCollection 2016.

6.

Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation.

Li M, Kales SC, Ma K, Shoemaker BA, Crespo-Barreto J, Cangelosi AL, Lipkowitz S, Panchenko AR.

Cancer Res. 2016 Feb 1;76(3):561-71. doi: 10.1158/0008-5472.CAN-14-3812. Epub 2015 Dec 16.

7.

PubChem Substance and Compound databases.

Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1202-13. doi: 10.1093/nar/gkv951. Epub 2015 Sep 22.

8.

Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.

Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR.

Biophys J. 2015 Sep 15;109(6):1295-306. doi: 10.1016/j.bpj.2015.06.056. Epub 2015 Jul 23.

9.

Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.

Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR.

Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):187-93. doi: 10.1016/j.pbiomolbio.2014.05.005. Epub 2014 Jun 13. Review.

10.

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.

11.

Cancer missense mutations alter binding properties of proteins and their interaction networks.

Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR.

PLoS One. 2013 Jun 14;8(6):e66273. doi: 10.1371/journal.pone.0066273. Print 2013.

12.

Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics.

Li M, Shoemaker BA, Thangudu RR, Ferraris JD, Burg MB, Panchenko AR.

J Phys Chem B. 2013 Oct 24;117(42):13226-34. doi: 10.1021/jp403310a. Epub 2013 Jun 25.

13.

Large-scale mapping of human protein interactome using structural complexes.

Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR.

EMBO Rep. 2012 Mar 1;13(3):266-71. doi: 10.1038/embor.2011.261.

14.

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.

15.

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.

16.

Intrinsic protein disorder in human pathways.

Fong JH, Shoemaker BA, Panchenko AR.

Mol Biosyst. 2012 Jan;8(1):320-6. doi: 10.1039/c1mb05274h. Epub 2011 Oct 20.

17.

Knowledge-based annotation of small molecule binding sites in proteins.

Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T.

BMC Bioinformatics. 2010 Jul 1;11:365. doi: 10.1186/1471-2105-11-365.

18.

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.

19.

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder.

Lobanov MY, Shoemaker BA, Garbuzynskiy SO, Fong JH, Panchenko AR, Galzitskaya OV.

Nucleic Acids Res. 2010 Jan;38(Database issue):D283-7. doi: 10.1093/nar/gkp963. Epub 2009 Nov 11.

20.

Evolution of protein binding modes in homooligomers.

Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR.

J Mol Biol. 2010 Jan 29;395(4):860-70. doi: 10.1016/j.jmb.2009.10.052. Epub 2009 Oct 30.

21.

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.

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

Nucleic Acids Res. 2010 Jan;38(Database issue):D518-24. doi: 10.1093/nar/gkp842. Epub 2009 Oct 20.

22.

Exploring functional roles of multibinding protein interfaces.

Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR.

Protein Sci. 2009 Aug;18(8):1674-83. doi: 10.1002/pro.181.

23.

Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis.

Fong JH, Shoemaker BA, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV, Panchenko AR.

PLoS Comput Biol. 2009 Mar;5(3):e1000316. doi: 10.1371/journal.pcbi.1000316. Epub 2009 Mar 13.

24.

Correlated evolution of interacting proteins: looking behind the mirrortree.

Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM.

J Mol Biol. 2009 Jan 9;385(1):91-8. doi: 10.1016/j.jmb.2008.09.078. Epub 2008 Oct 9.

25.
26.

Deciphering protein-protein interactions. Part I. Experimental techniques and databases.

Shoemaker BA, Panchenko AR.

PLoS Comput Biol. 2007 Mar 30;3(3):e42. Review. No abstract available.

27.

Finding biologically relevant protein domain interactions: conserved binding mode analysis.

Shoemaker BA, Panchenko AR, Bryant SH.

Protein Sci. 2006 Feb;15(2):352-61. Epub 2005 Dec 29.

28.

Histone structure and nucleosome stability.

Mariño-Ramírez L, Kann MG, Shoemaker BA, Landsman D.

Expert Rev Proteomics. 2005 Oct;2(5):719-29. Review.

29.

CDD: a Conserved Domain Database for protein classification.

Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6.

30.

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.

31.

CDD: a curated Entrez database of conserved domain alignments.

Marchler-Bauer A, 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 GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, 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):383-7.

32.

CDD: a database of conserved domain alignments with links to domain three-dimensional structure.

Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH.

Nucleic Acids Res. 2002 Jan 1;30(1):281-3.

33.

MMDB: Entrez's 3D-structure database.

Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH, Marchler-Bauer A, Panchenko AR, Shoemaker BA, Song JS, Thiessen PA, Yamashita RA, Bryant SH.

Nucleic Acids Res. 2002 Jan 1;30(1):249-52.

34.

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism.

Shoemaker BA, Portman JJ, Wolynes PG.

Proc Natl Acad Sci U S A. 2000 Aug 1;97(16):8868-73.

35.

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble.

Shoemaker BA, Wang J, Wolynes PG.

J Mol Biol. 1999 Apr 2;287(3):675-94.

PMID:
10092467
36.

Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble.

Shoemaker BA, Wolynes PG.

J Mol Biol. 1999 Apr 2;287(3):657-74.

PMID:
10092466
37.

Structural correlations in protein folding funnels.

Shoemaker BA, Wang J, Wolynes PG.

Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):777-82.

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