Benjamin A. Shoemaker, Ph.D. - Publications

Affiliations: 
University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
protein folding, regulatory networks, glasses, many-body phenomena

35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Wang Y, Bryant SH, Cheng T, Wang J, Gindulyte A, Shoemaker BA, Thiessen PA, He S, Zhang J. PubChem BioAssay: 2017 update. Nucleic Acids Research. PMID 27899599 DOI: 10.1093/nar/gkw1118  0.64
2016 Kim S, Thiessen PA, Cheng T, Yu B, Shoemaker BA, Wang J, Bolton EE, Wang Y, Bryant SH. Literature information in PubChem: associations between PubChem records and scientific articles. Journal of Cheminformatics. 8: 32. PMID 27293485 DOI: 10.1186/s13321-016-0142-6  0.64
2015 Li M, Kales SC, Ma K, Shoemaker B, Crespo-Barreto J, Cangelosi A, Lipkowitz S, Panchenko A. Balancing protein stability and activity in cancer: a new approach for identifying driver mutations affecting CBL ubiquitin ligase activation. Cancer Research. PMID 26676746 DOI: 10.1158/0008-5472.CAN-14-3812  1
2015 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. PubChem Substance and Compound databases. Nucleic Acids Research. PMID 26400175 DOI: 10.1093/nar/gkv951  1
2015 Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophysical Journal. 109: 1295-306. PMID 26213149 DOI: 10.1016/j.bpj.2015.06.056  1
2014 Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. Progress in Biophysics and Molecular Biology. 116: 187-93. PMID 24931138 DOI: 10.1016/j.pbiomolbio.2014.05.005  1
2014 Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH. PubChem BioAssay: 2014 update. Nucleic Acids Research. 42: D1075-82. PMID 24198245 DOI: 10.1093/nar/gkt978  1
2013 Shoemaker B, Wuchty S, Panchenko AR. Computational large-scale mapping of protein-protein interactions using structural complexes. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. 73: Unit 3.9. PMID 24510594 DOI: 10.1002/0471140864.ps0309s73  1
2013 Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR. Cancer missense mutations alter binding properties of proteins and their interaction networks. Plos One. 8: e66273. PMID 23799087 DOI: 10.1371/journal.pone.0066273  1
2013 Li M, Shoemaker BA, Thangudu RR, Ferraris JD, Burg MB, Panchenko AR. Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics. The Journal of Physical Chemistry. B. 117: 13226-34. PMID 23734591 DOI: 10.1021/jp403310a  1
2012 Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR. Large-scale mapping of human protein interactome using structural complexes. Embo Reports. 13: 266-71. PMID 22261719 DOI: 10.1038/embor.2011.261  1
2012 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. PubChem's BioAssay Database. Nucleic Acids Research. 40: D400-12. PMID 22140110 DOI: 10.1093/nar/gkr1132  1
2012 Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Research. 40: D834-40. PMID 22102591 DOI: 10.1093/nar/gkr997  1
2012 Fong JH, Shoemaker BA, Panchenko AR. Intrinsic protein disorder in human pathways. Molecular Biosystems. 8: 320-6. PMID 22012032 DOI: 10.1039/c1mb05274h  1
2010 Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T. Knowledge-based annotation of small molecule binding sites in proteins. Bmc Bioinformatics. 11: 365. PMID 20594344 DOI: 10.1186/1471-2105-11-365  1
2010 Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang J, Xiao J, Zhang J, Bryant SH. An overview of the PubChem BioAssay resource. Nucleic Acids Research. 38: D255-66. PMID 19933261 DOI: 10.1093/nar/gkp965  1
2010 Lobanov MY, Shoemaker BA, Garbuzynskiy SO, Fong JH, Panchenko AR, Galzitskaya OV. ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Research. 38: D283-7. PMID 19906708 DOI: 10.1093/nar/gkp963  1
2010 Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR. Evolution of protein binding modes in homooligomers. Journal of Molecular Biology. 395: 860-70. PMID 19879880 DOI: 10.1016/j.jmb.2009.10.052  1
2010 Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Research. 38: D518-24. PMID 19843613 DOI: 10.1093/nar/gkp842  1
2009 Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR. Exploring functional roles of multibinding protein interfaces. Protein Science : a Publication of the Protein Society. 18: 1674-83. PMID 19591200 DOI: 10.1002/pro.181  1
2009 Fong JH, Shoemaker BA, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV, Panchenko AR. Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. Plos Computational Biology. 5: e1000316. PMID 19282967 DOI: 10.1371/journal.pcbi.1000316  1
2009 Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM. Correlated evolution of interacting proteins: looking behind the mirrortree. Journal of Molecular Biology. 385: 91-8. PMID 18930732 DOI: 10.1016/j.jmb.2008.09.078  1
2007 Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. Plos Computational Biology. 3: e43. PMID 17465672 DOI: 10.1371/journal.pcbi.0030043  1
2007 Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part I. Experimental techniques and databases. Plos Computational Biology. 3: e42. PMID 17397251 DOI: 10.1371/journal.pcbi.0030042  1
2007 Wolf Y, Madej T, Babenko V, Shoemaker B, Panchenko AR. Long-term trends in evolution of indels in protein sequences. Bmc Evolutionary Biology. 7: 19. PMID 17298668 DOI: 10.1186/1471-2148-7-19  1
2006 Shoemaker BA, Panchenko AR, Bryant SH. Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Science : a Publication of the Protein Society. 15: 352-61. PMID 16385001 DOI: 10.1110/ps.051760806  1
2005 Mariño-Ramírez L, Kann MG, Shoemaker BA, Landsman D. Histone structure and nucleosome stability. Expert Review of Proteomics. 2: 719-29. PMID 16209651 DOI: 10.1586/14789450.2.5.719  1
2005 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, ... ... Shoemaker BA, et al. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Research. 33: D192-6. PMID 15608175 DOI: 10.1093/nar/gki069  1
2003 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, ... ... Shoemaker BA, et al. MMDB: Entrez's 3D-structure database. Nucleic Acids Research. 31: 474-7. PMID 12520055 DOI: 10.1093/nar/gkg086  1
2003 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, ... ... Shoemaker BA, et al. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Research. 31: 383-7. PMID 12520028 DOI: 10.1093/nar/gkg087  1
2002 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, et al. MMDB: Entrez's 3D-structure database. Nucleic Acids Research. 30: 249-52. PMID 11752307  1
2000 Shoemaker BA, Portman JJ, Wolynes PG. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proceedings of the National Academy of Sciences of the United States of America. 97: 8868-73. PMID 10908673 DOI: 10.1073/pnas.160259697  1
1999 Shoemaker BA, Wang J, Wolynes PG. Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble. Journal of Molecular Biology. 287: 675-94. PMID 10092467 DOI: 10.1006/jmbi.1999.2613  1
1999 Shoemaker BA, Wolynes PG. Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble. Journal of Molecular Biology. 287: 657-74. PMID 10092466 DOI: 10.1006/jmbi.1999.2612  1
1997 Shoemaker BA, Wang J, Wolynes PG. Structural correlations in protein folding funnels. Proceedings of the National Academy of Sciences of the United States of America. 94: 777-82. PMID 9023333 DOI: 10.1073/pnas.94.3.777  1
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