MMDB: An ASN.1 Specification for Macromolecular Structure. - Hitomi Ohkawa; James Ostell; Stephen H. Bryant (ISMB, 1995)

MMDB: Entrez's 3D structure database. - Aron Marchler-Bauer; Kenneth J. Addess; Colombe Chappey; Lewis Y. Geer; Thomas Madej; Yo Matsuo; Yanli Wang; Stephen H. Bryant (Nucleic Acids Res., 1999)

Domain size distributions can predict domain boundaries. - Sarah J. Wheelan; Aron Marchler-Bauer; Stephen H. Bryant (Bioinform., 2000)

MMDB: 3D structure data in Entrez. - Yanli Wang; Kenneth J. Addess; Lewis Y. Geer; Thomas Madej; Aron Marchler-Bauer; Diane Zimmerman; Stephen H. Bryant (Nucleic Acids Res., 2000)

CDD: a database of conserved domain alignments with links to domain three-dimensional structure. - Aron Marchler-Bauer; Anna R. Panchenko; Benjamin A. Shoemaker; Paul A. Thiessen; Lewis Y. Geer; Stephen H. Bryant (Nucleic Acids Res., 2002)

MMDB: Entrez's 3D-structure database. - Yanli Wang; John B. Anderson; Jie Chen 039; 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; et al. (Nucleic Acids Res., 2002)

MMDB: Entrez's 3D-structure database. - Jie Chen 039; John B. Anderson; Carol DeWeese-Scott; Natalie D. Fedorova; Lewis Y. Geer; Siqian He; David I. Hurwitz; John D. Jackson; Aviva R. Jacobs; Christopher J. Lanczycki; Cynthia A. Liebert; Chunlei Liu 002; et al. (Nucleic Acids Res., 2003)

CDD: a curated Entrez database of conserved domain alignments. - Aron Marchler-Bauer; John B. Anderson; Carol DeWeese-Scott; Natalie D. Fedorova; Lewis Y. Geer; Siqian He; David I. Hurwitz; John D. Jackson; Aviva R. Jacobs; Christopher J. Lanczycki; Cynthia A. Liebert; Chunlei Liu 002; et al. (Nucleic Acids Res., 2003)

CD-Search: protein domain annotations on the fly. - Aron Marchler-Bauer; Stephen H. Bryant (Nucleic Acids Res., 2004)

A structure-based method for protein sequence alignment. - Maricel G. Kann; Paul A. Thiessen; Anna R. Panchenko; Alejandro A. Schäffer; Stephen F. Altschul; Stephen H. Bryant (Bioinform., 2005)

CDD: a Conserved Domain Database for protein classification. - Aron Marchler-Bauer; John B. Anderson; Praveen F. Cherukuri; Carol DeWeese-Scott; Lewis Y. Geer; Marc Gwadz; Siqian He; David I. Hurwitz; John D. Jackson; Zhaoxi Ke; Christopher J. Lanczycki; Cynthia A. Liebert; et al. (Nucleic Acids Res., 2005)

Database resources of the National Center for Biotechnology Information. - David L. Wheeler; Tanya Barrett; Dennis A. Benson; Stephen H. Bryant; Kathi Canese; Deanna M. Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Wolfgang Helmberg; David L. Kenton; Oleg Khovayko; et al. (Nucleic Acids Res., 2005)

State of the art: refinement of multiple sequence alignments. - Saikat Chakrabarti 001; Christopher J. Lanczycki; Anna R. Panchenko; Teresa M. Przytycka; Paul A. Thiessen; Stephen H. Bryant (BMC Bioinform., 2006)

Database resources of the National Center for Biotechnology Information. - 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; et al. (Nucleic Acids Res., 2006)

Assessment of Conformational Ensemble Sizes Necessary for Specific Resolutions of Coverage of Conformational Space. - Yulia V. Borodina; Evan Bolton; Fabien Fontaine; Stephen H. Bryant (J. Chem. Inf. Model., 2007)

CDD: a conserved domain database for interactive domain family analysis. - Aron Marchler-Bauer; John B. Anderson; Myra K. Derbyshire; Carol DeWeese-Scott; Noreen R. Gonzales; Marc Gwadz; Luning Hao; Siqian He; David I. Hurwitz; John D. Jackson; Zhaoxi Ke; Dmitri M. Krylov; et al. (Nucleic Acids Res., 2007)

MMDB: annotating protein sequences with Entrez's 3D-structure database. - Yanli Wang; Kenneth J. Addess; Jie Chen 039; Lewis Y. Geer; Jane He; Siqian He; Shennan Lu; Thomas Madej; Aron Marchler-Bauer; Paul A. Thiessen; Naigong Zhang; Stephen H. Bryant (Nucleic Acids Res., 2007)

Database resources of the National Center for Biotechnology Information. - 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; Yuri Kapustin; et al. (Nucleic Acids Res., 2007)

Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. - Lianyi Han; Yanli Wang; Stephen H. Bryant (BMC Bioinform., 2008)

Database resources of the National Center for Biotechnology Information. - David L. Wheeler; Tanya Barrett; Dennis A. Benson; Stephen H. Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M. Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Michael Feolo; Lewis Y. Geer; et al. (Nucleic Acids Res., 2008)

PubChem: The NIH Public Repository for Small Molecules and Biological Screening Results. - Yanli Wang; Stephen H. Bryant (BIOCOMP, 2009)

A survey of across-target bioactivity results of small molecules in PubChem. - Lianyi Han; Yanli Wang; Stephen H. Bryant (Bioinform., 2009)

A novel method for mining highly imbalanced high-throughput screening data in PubChem. - Qingliang Li; Yanli Wang; Stephen H. Bryant (Bioinform., 2009)

Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex. - Zhigang Zhou; Yanli Wang; Stephen H. Bryant (J. Comput. Chem., 2009)

The PubChem chemical structure sketcher. - Wolf-Dietrich Ihlenfeldt; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2009)

CDD: specific functional annotation with the Conserved Domain Database. - Aron Marchler-Bauer; John B. Anderson; Farideh Chitsaz; Myra K. Derbyshire; Carol DeWeese-Scott; Jessica H. Fong; Lewis Y. Geer; Renata C. Geer; Noreen R. Gonzales; Marc Gwadz; Siqian He; David I. Hurwitz; et al. (Nucleic Acids Res., 2009)

Database resources of the National Center for Biotechnology Information. - Eric W. Sayers; Tanya Barrett; Dennis A. Benson; Stephen H. Bryant; Kathi Canese; Vyacheslav Chetvernin; Deanna M. Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Michael Feolo; Lewis Y. Geer; et al. (Nucleic Acids Res., 2009)

PubChem: a public information system for analyzing bioactivities of small molecules. - Yanli Wang; Jewen Xiao; Tugba O. Suzek; Jian Zhang 038; Jiyao Wang; Stephen H. Bryant (Nucleic Acids Res., 2009)

Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules. - Tiejun Cheng; Yanli Wang; Stephen H. Bryant (Bioinform., 2010)

Knowledge-based annotation of small molecule binding sites in proteins. - Ratna R. Thangudu; Manoj Tyagi; Benjamin A. Shoemaker; Stephen H. Bryant; Anna R. Panchenko; Thomas Madej (BMC Bioinform., 2010)

The NCBI BioSystems database. - Lewis Y. Geer; Aron Marchler-Bauer; Renata C. Geer; Lianyi Han; Jane He; Siqian He; Chunlei Liu 002; Wenyao Shi; Stephen H. Bryant (Nucleic Acids Res., 2010)

Database resources of the National Center for Biotechnology Information. - 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; Lewis Y. Geer; et al. (Nucleic Acids Res., 2010)

Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites. - Benjamin A. Shoemaker; Dachuan Zhang; Ratna R. Thangudu; Manoj Tyagi; Jessica H. Fong; Aron Marchler-Bauer; Stephen H. Bryant; Tom Madej; Anna R. Panchenko (Nucleic Acids Res., 2010)

An overview of the PubChem BioAssay resource. - Yanli Wang; Evan Bolton; Svetlana Dracheva; Karen Karapetyan; Benjamin A. Shoemaker; Tugba O. Suzek; Jiyao Wang; Jewen Xiao; Jian Zhang 038; Stephen H. Bryant (Nucleic Acids Res., 2010)

Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. - Viswanadham Sridhara; Aron Marchler-Bauer; Stephen H. Bryant; Lewis Y. Geer (Database J. Biol. Databases Curation, 2011)

PubChem3D: a new resource for scientists. - Evan Bolton; Jie Chen 039; Sunghwan Kim 002; Lianyi Han; Siqian He; Wenyao Shi; Vahan Simonyan; Yan Sun; Paul A. Thiessen; Jiyao Wang; Bo Yu 016; Jian Zhang 038; et al. (J. Cheminformatics, 2011)

PubChem3D: Conformer generation. - Evan Bolton; Sunghwan Kim 002; Stephen H. Bryant (J. Cheminformatics, 2011)

PubChem3D: Diversity of shape. - Evan Bolton; Sunghwan Kim 002; Stephen H. Bryant (J. Cheminformatics, 2011)

PubChem3D: Similar conformers. - Evan Bolton; Sunghwan Kim 002; Stephen H. Bryant (J. Cheminformatics, 2011)

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles. - Sunghwan Kim 002; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2011)

PubChem3D: Biologically relevant 3-D similarity. - Sunghwan Kim 002; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2011)

Automated annotation of chemical names in the literature with tunable accuracy. - Jun D. Zhang; Lewis Y. Geer; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2011)

Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection. - Tiejun Cheng; Qingliang Li; Yanli Wang; Stephen H. Bryant (J. Chem. Inf. Model., 2011)

Identifying Compound-Target Associations by Combining Bioactivity Profile Similarity Search and Public Databases Mining. - Tiejun Cheng; Qingliang Li; Yanli Wang; Stephen H. Bryant (J. Chem. Inf. Model., 2011)

CDD: a Conserved Domain Database for the functional annotation of proteins. - Aron Marchler-Bauer; Shennan Lu; John B. Anderson; Farideh Chitsaz; Myra K. Derbyshire; Carol DeWeese-Scott; Jessica H. Fong; Lewis Y. Geer; Renata C. Geer; Noreen R. Gonzales; Marc Gwadz; David I. Hurwitz; et al. (Nucleic Acids Res., 2011)

Database resources of the National Center for Biotechnology Information. - 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; et al. (Nucleic Acids Res., 2011)

Annotation of functional sites with the Conserved Domain Database. - Myra K. Derbyshire; Christopher J. Lanczycki; Stephen H. Bryant; Aron Marchler-Bauer (Database J. Biol. Databases Curation, 2012)

FSelector: a Ruby gem for feature selection. - Tiejun Cheng; Yanli Wang; Stephen H. Bryant (Bioinform., 2012)

Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis. - Sunghwan Kim 002; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2012)

MMDB: 3D structures and macromolecular interactions. - Thomas Madej; Kenneth J. Addess; Jessica H. Fong; Lewis Y. Geer; Renata C. Geer; Christopher J. Lanczycki; Chunlei Liu 002; Shennan Lu; Aron Marchler-Bauer; Anna R. Panchenko; Jie Chen 039; Paul A. Thiessen; et al. (Nucleic Acids Res., 2012)

Database resources of the National Center for Biotechnology Information. - 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; et al. (Nucleic Acids Res., 2012)

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. - Benjamin A. Shoemaker; Dachuan Zhang; Manoj Tyagi; Ratna R. Thangudu; Jessica H. Fong; Aron Marchler-Bauer; Stephen H. Bryant; Thomas Madej; Anna R. Panchenko (Nucleic Acids Res., 2012)

PubChem's BioAssay Database. - Yanli Wang; Jewen Xiao; Tugba O. Suzek; Jian Zhang 038; Jiyao Wang; Zhigang Zhou; Lianyi Han; Karen Karapetyan; Svetlana Dracheva; Benjamin A. Shoemaker; Evan Bolton; Asta Gindulyte; et al. (Nucleic Acids Res., 2012)

PubChem: atom environments for molecule standardization. - Volker Hähnke; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2013)

PubChem3D: conformer ensemble accuracy. - Sunghwan Kim 002; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2013)

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. - Yongmei Pan; Yanli Wang; Stephen H. Bryant (J. Chem. Inf. Model., 2013)

CDD: conserved domains and protein three-dimensional structure. - Aron Marchler-Bauer; Chanjuan Zheng; Farideh Chitsaz; Myra K. Derbyshire; Lewis Y. Geer; Renata C. Geer; Noreen R. Gonzales; Marc Gwadz; David I. Hurwitz; Christopher J. Lanczycki; Fu Lu; Shennan Lu; et al. (Nucleic Acids Res., 2013)

Pathway Analysis for Drug Repositioning Based on Public Database Mining. - Yongmei Pan; Tiejun Cheng; Yanli Wang; Stephen H. Bryant (J. Chem. Inf. Model., 2014)

MMDB and VAST+: tracking structural similarities between macromolecular complexes. - Thomas Madej; Christopher J. Lanczycki; Dachuan Zhang; Paul A. Thiessen; Renata C. Geer; Aron Marchler-Bauer; Stephen H. Bryant (Nucleic Acids Res., 2014)

PubChem BioAssay: 2014 update. - Yanli Wang; Tugba O. Suzek; Jian Zhang 038; Jiyao Wang; Siqian He; Tiejun Cheng; Benjamin A. Shoemaker; Asta Gindulyte; Stephen H. Bryant (Nucleic Acids Res., 2014)

PubChem atom environments. - Volker Hähnke; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2015)

PubChem structure-activity relationship (SAR) clusters. - Sunghwan Kim 002; Lianyi Han; Bo Yu 016; Volker Hähnke; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2015)

Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. - Xiang Yu; Lewis Y. Geer; Lianyi Han; Stephen H. Bryant (J. Cheminformatics, 2015)

PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. - Sunghwan Kim 002; Paul A. Thiessen; Evan Bolton; Stephen H. Bryant (Nucleic Acids Res., 2015)

CDD: NCBI's conserved domain database. - Aron Marchler-Bauer; Myra K. Derbyshire; Noreen R. Gonzales; Shennan Lu; Farideh Chitsaz; Lewis Y. Geer; Renata C. Geer; Jane He; Marc Gwadz; David I. Hurwitz; Christopher J. Lanczycki; Fu Lu; et al. (Nucleic Acids Res., 2015)

Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold. - Takako Takeda; Yanli Wang; Stephen H. Bryant (J. Comput. Aided Mol. Des., 2016)

Literature information in PubChem: associations between PubChem records and scientific articles. - Sunghwan Kim 002; Paul A. Thiessen; Tiejun Cheng; Bo Yu 016; Benjamin A. Shoemaker; Jiyao Wang; Evan Bolton; Yanli Wang; Stephen H. Bryant (J. Cheminformatics, 2016)

Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem. - Ming Hao; Stephen H. Bryant; Yanli Wang (J. Cheminformatics, 2016)

Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. - Sunghwan Kim 002; Evan Bolton; Stephen H. Bryant (J. Cheminformatics, 2016)

PubChem Substance and Compound databases. - Sunghwan Kim 002; Paul A. Thiessen; Evan Bolton; Jie Chen 039; Gang Fu; Asta Gindulyte; Lianyi Han; Jane He; Siqian He; Benjamin A. Shoemaker; Jiyao Wang; Bo Yu 016; et al. (Nucleic Acids Res., 2016)

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. - Amrita Roy Choudhury; Tiejun Cheng; Lon Phan; Stephen H. Bryant; Yanli Wang (Bioinform., 2017)

Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. - Takako Takeda; Ming Hao; Tiejun Cheng; Stephen H. Bryant; Yanli Wang (J. Cheminformatics, 2017)

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. - Aron Marchler-Bauer; Bo Yu 016; Lianyi Han; Jane He; Christopher J. Lanczycki; Shennan Lu; Farideh Chitsaz; Myra K. Derbyshire; Renata C. Geer; Noreen R. Gonzales; Marc Gwadz; David I. Hurwitz; et al. (Nucleic Acids Res., 2017)

PubChem BioAssay: 2017 update. - Yanli Wang; Stephen H. Bryant; Tiejun Cheng; Jiyao Wang; Asta Gindulyte; Benjamin A. Shoemaker; Paul A. Thiessen; Siqian He; Jian Zhang 038 (Nucleic Acids Res., 2017)

A new chemoinformatics approach with improved strategies for effective predictions of potential drugs. - Ming Hao; Stephen H. Bryant; Yanli Wang (J. Cheminformatics, 2018)

Open-source chemogenomic data-driven algorithms for predicting drug-target interactions. - Ming Hao; Stephen H. Bryant; Yanli Wang (Briefings Bioinform., 2019)

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. - 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; et al. (Bioinform., 2020)