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Stephen H. Bryant
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- affiliation: National Center for Biotechnology Information, Bethesda, USA
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2020 – today
- 2020
- [j76]Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J. Lanczycki, Renata C. Geer, Thomas Madej, Lon Phan, Minghong Ward, Shennan Lu, Gabriele H. Marchler, Yanli Wang, Stephen H. Bryant, Lewis Y. Geer
, Aron Marchler-Bauer:
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. Bioinform. 36(1): 131-135 (2020)
2010 – 2019
- 2019
- [j75]Ming Hao, Stephen H. Bryant, Yanli Wang:
Open-source chemogenomic data-driven algorithms for predicting drug-target interactions. Briefings Bioinform. 20(4): 1465-1474 (2019) - 2018
- [j74]Ming Hao
A new chemoinformatics approach with improved strategies for effective predictions of potential drugs. J. Cheminformatics 10(1): 50:1-50:9 (2018) - 2017
- [j73]Amrita Roy Choudhury, Tiejun Cheng, Lon Phan, Stephen H. Bryant, Yanli Wang:
Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites. Bioinform. 33(11): 1621-1629 (2017) - [j72]Takako Takeda, Ming Hao
Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. J. Cheminformatics 9(1): 16:1-16:9 (2017) - [j71]Aron Marchler-Bauer
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 45(Database-Issue): D200-D203 (2017) - [j70]Yanli Wang, Stephen H. Bryant, Tiejun Cheng, Jiyao Wang, Asta Gindulyte, Benjamin A. Shoemaker, Paul A. Thiessen, Siqian He, Jian Zhang:
PubChem BioAssay: 2017 update. Nucleic Acids Res. 45(Database-Issue): D955-D963 (2017) - 2016
- [j69]Takako Takeda, Yanli Wang, Stephen H. Bryant:
Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold. J. Comput. Aided Mol. Des. 30(4): 323-330 (2016) - [j68]Sunghwan Kim
Literature information in PubChem: associations between PubChem records and scientific articles. J. Cheminformatics 8(1): 32:1-32:15 (2016) - [j67]Ming Hao
Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem. J. Cheminformatics 8(1): 37:1-37:13 (2016) - [j66]Sunghwan Kim
Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. J. Cheminformatics 8(1): 62:1-62:17 (2016) - [j65]Sunghwan Kim
PubChem Substance and Compound databases. Nucleic Acids Res. 44(Database-Issue): 1202-1213 (2016) - 2015
- [j64]Sunghwan Kim
PubChem structure-activity relationship (SAR) clusters. J. Cheminformatics 7: 33:1-33:22 (2015) - [j63]Volker Hähnke, Evan Bolton
PubChem atom environments. J. Cheminformatics 7: 41:1-41:37 (2015) - [j62]Xiang Yu, Lewis Y. Geer
Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. J. Cheminformatics 7: 55:1-55:12 (2015) - [j61]Aron Marchler-Bauer
CDD: NCBI's conserved domain database. Nucleic Acids Res. 43(Database-Issue): 222-226 (2015) - [j60]Sunghwan Kim
PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic Acids Res. 43(Webserver-Issue): W605-W611 (2015) - 2014
- [j59]Yongmei Pan, Tiejun Cheng
Pathway Analysis for Drug Repositioning Based on Public Database Mining. J. Chem. Inf. Model. 54(2): 407-418 (2014) - [j58]Thomas Madej, Christopher J. Lanczycki, Dachuan Zhang, Paul A. Thiessen, Renata C. Geer, Aron Marchler-Bauer
MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 42(Database-Issue): 297-303 (2014) - [j57]Yanli Wang, Tugba O. Suzek
PubChem BioAssay: 2014 update. Nucleic Acids Res. 42(Database-Issue): 1075-1082 (2014) - 2013
- [j56]Sunghwan Kim
PubChem3D: conformer ensemble accuracy. J. Cheminformatics 5: 1 (2013) - [j55]Volker Hähnke, Evan Bolton
PubChem: atom environments for molecule standardization. J. Cheminformatics 5(S-1): 38 (2013) - [j54]Yongmei Pan, Yanli Wang, Stephen H. Bryant:
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. J. Chem. Inf. Model. 53(4): 938-947 (2013) - [j53]Aron Marchler-Bauer
CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 41(Database-Issue): 348-352 (2013) - 2012
- [j52]Myra K. Derbyshire, Christopher J. Lanczycki, Stephen H. Bryant, Aron Marchler-Bauer
Annotation of functional sites with the Conserved Domain Database. Database J. Biol. Databases Curation 2012 (2012) - [j51]Tiejun Cheng
FSelector: a Ruby gem for feature selection. Bioinform. 28(21): 2851-2852 (2012) - [j50]Sunghwan Kim
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis. J. Cheminformatics 4: 28 (2012) - [j49]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40(Database-Issue): 13-25 (2012) - [j48]Yanli Wang, Jewen Xiao, Tugba O. Suzek
PubChem's BioAssay Database. Nucleic Acids Res. 40(Database-Issue): 400-412 (2012) - [j47]Thomas Madej, Kenneth J. Addess, Jessica H. Fong, Lewis Y. Geer
MMDB: 3D structures and macromolecular interactions. Nucleic Acids Res. 40(Database-Issue): 461-464 (2012) - [j46]Benjamin A. Shoemaker, Dachuan Zhang, Manoj Tyagi, Ratna R. Thangudu, Jessica H. Fong, Aron Marchler-Bauer
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Res. 40(Database-Issue): 834-840 (2012) - 2011
- [j45]Viswanadham Sridhara
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. Database J. Biol. Databases Curation 2011 (2011) - [j44]Evan Bolton
PubChem3D: Conformer generation. J. Cheminformatics 3: 4 (2011) - [j43]Evan Bolton
PubChem3D: Diversity of shape. J. Cheminformatics 3: 9 (2011) - [j42]Evan Bolton
PubChem3D: Similar conformers. J. Cheminformatics 3: 13 (2011) - [j41]Sunghwan Kim
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles. J. Cheminformatics 3: 25 (2011) - [j40]Sunghwan Kim
PubChem3D: Biologically relevant 3-D similarity. J. Cheminformatics 3: 26 (2011) - [j39]Evan Bolton
PubChem3D: a new resource for scientists. J. Cheminformatics 3: 32 (2011) - [j38]Jun D. Zhang, Lewis Y. Geer
Automated annotation of chemical names in the literature with tunable accuracy. J. Cheminformatics 3: 52 (2011) - [j37]Tiejun Cheng
Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection. J. Chem. Inf. Model. 51(2): 229-236 (2011) - [j36]Tiejun Cheng
Identifying Compound-Target Associations by Combining Bioactivity Profile Similarity Search and Public Databases Mining. J. Chem. Inf. Model. 51(9): 2440-2448 (2011) - [j35]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Ian M. Fingerman, Lewis Y. Geer
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39(Database-Issue): 38-51 (2011) - [j34]Aron Marchler-Bauer
CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 39(Database-Issue): 225-229 (2011) - 2010
- [j33]Tiejun Cheng
Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules. Bioinform. 26(22): 2881-2888 (2010) - [j32]Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka
State of the art: refinement of multiple sequence alignments. BMC Bioinform. 11: 3 (2010) - [j31]Ratna R. Thangudu, Manoj Tyagi, Benjamin A. Shoemaker, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej:
Knowledge-based annotation of small molecule binding sites in proteins. BMC Bioinform. 11: 365 (2010) - [j30]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 38(Database-Issue): 5-16 (2010) - [j29]Yanli Wang, Evan Bolton
An overview of the PubChem BioAssay resource. Nucleic Acids Res. 38(Database-Issue): 255-266 (2010) - [j28]Lewis Y. Geer
The NCBI BioSystems database. Nucleic Acids Res. 38(Database-Issue): 492-496 (2010) - [j27]Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer
Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Res. 38(Database-Issue): 518-524 (2010)
2000 – 2009
- 2009
- [j26]Lianyi Han
A survey of across-target bioactivity results of small molecules in PubChem. Bioinform. 25(17): 2251-2255 (2009) - [j25]Qingliang Li
A novel method for mining highly imbalanced high-throughput screening data in PubChem. Bioinform. 25(24): 3310-3316 (2009) - [j24]Zhigang Zhou, Yanli Wang, Stephen H. Bryant:
Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex. J. Comput. Chem. 30(14): 2165-2175 (2009) - [j23]Wolf-Dietrich Ihlenfeldt, Evan Bolton
The PubChem chemical structure sketcher. J. Cheminformatics 1: 20 (2009) - [j22]Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37(Database-Issue): 5-15 (2009) - [j21]Aron Marchler-Bauer
CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 37(Database-Issue): 205-210 (2009) - [j20]Yanli Wang, Jewen Xiao, Tugba O. Suzek
PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 37(Web-Server-Issue): 623-633 (2009) - [c2]Yanli Wang, Stephen H. Bryant:
PubChem: The NIH Public Repository for Small Molecules and Biological Screening Results. BIOCOMP 2009: 726-728 - 2008
- [j19]Lianyi Han
Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. BMC Bioinform. 9 (2008) - [j18]David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36(Database-Issue): 13-21 (2008) - 2007
- [j17]Yulia V. Borodina
Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space. J. Chem. Inf. Model. 47(4): 1428-1437 (2007) - [j16]David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35(Database-Issue): 5-12 (2007) - [j15]Aron Marchler-Bauer
CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35(Database-Issue): 237-240 (2007) - [j14]Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer
MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res. 35(Database-Issue): 298-300 (2007) - 2006
- [j13]Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. Panchenko, Teresa M. Przytycka
State of the art: refinement of multiple sequence alignments. BMC Bioinform. 7: 499 (2006) - [j12]David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David L. Kenton, Oleg Khovayko
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 34(Database-Issue): 173-180 (2006) - 2005
- [j11]Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant:
A structure-based method for protein sequence alignment. Bioinform. 21(8): 1451-1456 (2005) - [j10]David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33(Database-Issue): 39-45 (2005) - [j9]Aron Marchler-Bauer
CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33(Database-Issue): 192-196 (2005) - 2004
- [j8]Aron Marchler-Bauer
CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32(Web-Server-Issue): 327-331 (2004) - 2003
- [j7]Aron Marchler-Bauer
CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31(1): 383-387 (2003) - [j6]Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer
MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31(1): 474-477 (2003) - 2002
- [j5]Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant:
MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 30(1): 249-252 (2002) - [j4]Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A. Thiessen, Lewis Y. Geer
CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30(1): 281-283 (2002) - 2000
- [j3]Sarah J. Wheelan, Aron Marchler-Bauer, Stephen H. Bryant:
Domain size distributions can predict domain boundaries. Bioinform. 16(7): 613-618 (2000) - [j2]Yanli Wang, Kenneth J. Addess, Lewis Y. Geer, Thomas Madej, Aron Marchler-Bauer, Diane Zimmerman, Stephen H. Bryant:
MMDB: 3D structure data in Entrez. Nucleic Acids Res. 28(1): 243-245 (2000)
1990 – 1999
- 1999
- [j1]Aron Marchler-Bauer
MMDB: Entrez's 3D structure database. Nucleic Acids Res. 27(1): 240-243 (1999) - 1995
- [c1]Hitomi Ohkawa, James Ostell, Stephen H. Bryant:
MMDB: An ASN.1 Specification for Macromolecular Structure. ISMB 1995: 259-267
Coauthor Index
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