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Stephen Bryant

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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.
Sunghwan Kim; Evan E Bolton; Stephen H Bryant
PubChem3D: conformer ensemble accuracy.
Aron Marchler-Bauer; James S Song; Narmada Thanki; Roxanne A Yamashita; Dachuan Zhang; 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; Gabriele H Marchler; Stephen H Bryant
CDD: conserved domains and protein three-dimensional structure.

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All Publications

2013: 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.
Journal of chemical information and modeling 2013;53(4):938-47.
2013: Sunghwan Kim; Evan E Bolton; Stephen H Bryant
PubChem3D: conformer ensemble accuracy.
Journal of cheminformatics 2013;5(1):1.
2013: Aron Marchler-Bauer; James S Song; Narmada Thanki; Roxanne A Yamashita; Dachuan Zhang; 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; Gabriele H Marchler; Stephen H Bryant
CDD: conserved domains and protein three-dimensional structure.
Nucleic acids research 2013;41(Database issue):D348-52.
2012: Tiejun Cheng; Qingliang Li; Yanli Wang; Zhigang Zhou; Stephen H Bryant
Structure-based virtual screening for drug discovery: a problem-centric review.
The AAPS journal 2012;14(1):133-41.
2012: Arvind Chopra; W C Eckelman; Martin Latterner; Kam Leung; Stephen H Bryant; Liang Shan; Anne Menkens
Molecular Imaging and Contrast Agent Database (MICAD): evolution and progress.
Molecular imaging and biology : MIB : the official publication of the Academy of Molecular Imaging 2012;14(1):4-13.
2012: Sunghwan Kim; Evan E Bolton; Stephen H Bryant
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis.
Journal of cheminformatics 2012;4(1):28.
2012: Myra K Derbyshire; Christopher J Lanczycki; Stephen H Bryant; Aron Marchler-Bauer
Annotation of functional sites with the Conserved Domain Database.
Database : the journal of biological databases and curation 2012;2012():bar058.
2012: Viswanadham Sridhara; Donald F Hunt; Jeffrey Shabanowitz; Dina L Bai; Stephen H Bryant; An Chi; Lewis Y Geer
Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge.
Proteome science 2012;10(1):8.
2012: Manoj Tyagi; Dachuan Zhang; Stephen H Bryant; Thomas Madej; Ratna R Thangudu; Anna R Panchenko
Homology inference of protein-protein interactions via conserved binding sites.
PloS one 2012;7(1):e28896.
2011: Tiejun Cheng; Qingliang Li; Yanli Wang; Stephen H Bryant
Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining.
Journal of chemical information and modeling 2011;51(9):2440-8.
2011: Zhigang Zhou; Yanli Wang; Stephen H Bryant
Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors.
Journal of molecular graphics & modelling 2011;30():135-47.
2011: Tiejun Cheng; Qingliang Li; Yanli Wang; Stephen H Bryant
Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection.
Journal of chemical information and modeling 2011;51(2):229-36.
2011: Jun D Zhang; Lewis Y Geer; Evan E Bolton; Stephen H Bryant
Automated annotation of chemical names in the literature with tunable accuracy.
Journal of cheminformatics 2011;3(1):52.
2011: Evan E Bolton; Jie Chen; Lianyi Han; Siqian He; Sunghwan Kim; Wenyao Shi; Vahan Simonyan; Yan Sun; Paul A Thiessen; Jiyao Wang; Bo Yu; Jian Zhang; Stephen H Bryant
PubChem3D: a new resource for scientists.
Journal of cheminformatics 2011;3(1):32.
2011: Sunghwan Kim; Evan E Bolton; Stephen H Bryant
PubChem3D: Biologically relevant 3-D similarity.
Journal of cheminformatics 2011;3(1):26.
2011: Sunghwan Kim; Evan E Bolton; Stephen H Bryant
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles.
Journal of cheminformatics 2011;3():25.
2011: Viswanadham Sridhara; Aron Marchler-Bauer; Stephen H Bryant; Lewis Y Geer
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes.
Database : the journal of biological databases and curation 2011;2011():bar019.
2011: Evan E Bolton; Sunghwan Kim; Stephen H Bryant
PubChem3D: Similar conformers.
Journal of cheminformatics 2011;3():13.
2011: Evan E Bolton; Sunghwan Kim; Stephen H Bryant
PubChem3D: Diversity of shape.
Journal of cheminformatics 2011;3():9.
2011: Evan E Bolton; Sunghwan Kim; Stephen H Bryant
PubChem3D: Conformer generation.
Journal of cheminformatics 2011;3(1):4.
2011: 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; John D Jackson; Zhaoxi Ke; Christopher J Lanczycki; Fu Lu; Gabriele H Marchler; Mikhail Mullokandov; Marina V Omelchenko; Cynthia L Robertson; James S Song; Narmada Thanki; Roxanne A Yamashita; Dachuan Zhang; Naigong Zhang; Chanjuan Zheng; Stephen H Bryant
CDD: a Conserved Domain Database for the functional annotation of proteins.
Nucleic acids research 2011;39(Database issue):D225-9.
2010: Qingliang Li; Tiejun Cheng; Yanli Wang; Stephen H Bryant
PubChem as a public resource for drug discovery.
Drug discovery today 2010;15(23-24):1052-7.
2010: Tiejun Cheng; Yanli Wang; Stephen H Bryant
Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules.
Bioinformatics (Oxford, England) 2010;26(22):2881-8.
2010: Zhigang Zhou; Yanli Wang; Stephen H Bryant
QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules.
Journal of molecular graphics & modelling 2010;28(8):714-27.
2010: Kosuke Hashimoto; Thomas Madej; Stephen H Bryant; Anna R Panchenko
Functional states of homooligomers: insights from the evolution of glycosyltransferases.
Journal of molecular biology 2010;399(1):196-206.
2010: Lianyi Han; Tugba O Suzek; Yanli Wang; Stephen H Bryant
The Text-mining based PubChem Bioassay neighboring analysis.
BMC bioinformatics 2010;11():549.
2010: 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 bioinformatics 2010;11():365.
2010: Yanli Wang; Evan Bolton; Svetlana Dracheva; Karen Karapetyan; Benjamin A Shoemaker; Tugba O Suzek; Jiyao Wang; Jewen Xiao; J Zhang; Stephen H Bryant
An overview of the PubChem BioAssay resource.
Nucleic acids research 2010;38(Database issue):D255-66.
2010: Lewis Y Geer; Aron Marchler-Bauer; Renata C Geer; Lianyi Han; Jane He; Siqian He; Chunlei Liu; Wenyao Shi; Stephen H Bryant
The NCBI BioSystems database.
Nucleic acids research 2010;38(Database issue):D492-6.
2010: Benjamin A Shoemaker; Dachuan Zhang; Ratna R Thangudu; Manoj Tyagi; Jessica H Fong; Aron Marchler-Bauer; Stephen H Bryant; Thomas Madej; Anna R Panchenko
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.
Nucleic acids research 2010;38(Database issue):D518-24.
2009: Qingliang Li; Yanli Wang; Stephen H Bryant
A novel method for mining highly imbalanced high-throughput screening data in PubChem.
Bioinformatics (Oxford, England) 2009;25(24):3310-6.
2009: 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.
Journal of computational chemistry 2009;30(14):2165-75.
2009: Lianyi Han; Yanli Wang; Stephen H Bryant
A survey of across-target bioactivity results of small molecules in PubChem.
Bioinformatics (Oxford, England) 2009;25(17):2251-5.
2009: Manoj Tyagi; Benjamin A Shoemaker; Stephen H Bryant; Anna R Panchenko
Exploring functional roles of multibinding protein interfaces.
Protein science : a publication of the Protein Society 2009;18(8):1674-83.
2009: Yanli Wang; Jewen Xiao; Tugba O Suzek; J Zhang; Jiyao Wang; Stephen H Bryant
PubChem: a public information system for analyzing bioactivities of small molecules.
Nucleic acids research 2009;37(Web Server issue):W623-33.
2009: Wolf D Ihlenfeldt; Evan E Bolton; Stephen H Bryant
The PubChem chemical structure sketcher.
Journal of cheminformatics 2009;1(1):20.
2009: Kenneth Evan Thompson; Yanli Wang; Thomas Madej; Stephen H Bryant
Improving protein structure similarity searches using domain boundaries based on conserved sequence information.
BMC structural biology 2009;9():33.
2008: Lianyi Han; Yanli Wang; Stephen H Bryant
Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem.
BMC bioinformatics 2008;9():401.
2007: Saikat Chakrabarti; Stephen H Bryant; Anna R Panchenko
Functional specificity lies within the properties and evolutionary changes of amino acids.
Journal of molecular biology 2007;373(3):801-10.
2007: Yulia V Borodina; Evan Bolton; Fabien Fontaine; Stephen H Bryant
Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space.
Journal of chemical information and modeling 2007;47(4):1428-37.
2007: Jessica H Fong; Lewis Y Geer; Anna R Panchenko; Stephen H Bryant
Modeling the evolution of protein domain architectures using maximum parsimony.
Journal of molecular biology 2007;366(1):307-15.
2007: Fabien Fontaine; Evan Bolton; Yulia Borodina; Stephen H Bryant
Fast 3D shape screening of large chemical databases through alignment-recycling.
Chemistry Central journal 2007;1():12.
2007: Maricel G Kann; Sergey L Sheetlin; Yonil Park; Stephen H Bryant; John L Spouge
The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.
Nucleic acids research 2007;35(14):4678-85.
2007: Thomas Madej; Anna R Panchenko; Jie Chen; Stephen H Bryant
Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins.
BMC structural biology 2007;7():23.
2007: david 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; Oleg Khovayko; David Landsman; David Lipman; Thomas L Madden; Donna R Maglott; James Ostell; Vadim Miller; Kim D Pruitt; Gerold Schuler; Edwin Sequeira; Stephen T Sherry; Karl Sirotkin; Alexander Souvorov; Grigory Starchenko; Roman L Tatusov; Tatiana Tatusova; Lukas Wagner; Eugene Yaschenko
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2007;35(Database issue):D5-12.
2007: 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; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Fu Lu; Shennan Lu; Gabriele H Marchler; Mikhail Mullokandov; James S Song; Narmada Thanki; Roxanne A Yamashita; Jodie Yin; Dachuan Zhang; Stephen H Bryant
CDD: a conserved domain database for interactive domain family analysis.
Nucleic acids research 2007;35(Database issue):D237-40.
2007: Yanli Wang; Kenneth J Addess; Jie Chen; Lewis Y Geer; Jane He; Siqian He; Shennan Lu; Thomas Madej; Aron Marchler-Bauer; Paul A Thiessen; Naigong Zhang; Stephen H Bryant
MMDB: annotating protein sequences with Entrez's 3D-structure database.
Nucleic acids research 2007;35(Database issue):D298-300.
2006: Benjamin A Shoemaker; Anna R Panchenko; Stephen H Bryant
Finding biologically relevant protein domain interactions: conserved binding mode analysis.
Protein science : a publication of the Protein Society 2006;15(2):352-61.
2006: Saikat Chakrabarti; Christopher J Lanczycki; Anna R Panchenko; Teresa M Przytycka; Paul A Thiessen; Stephen H Bryant
State of the art: refinement of multiple sequence alignments.
BMC bioinformatics 2006;7():499.
2006: Saikat Chakrabarti; Christopher J Lanczycki; Anna R Panchenko; Teresa M Przytycka; Paul A Thiessen; Stephen H Bryant
Refining multiple sequence alignments with conserved core regions.
Nucleic acids research 2006;34(9):2598-606.
2005: 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.
Bioinformatics (Oxford, England) 2005;21(8):1451-6.
2005: Ming Xu; Lewis Y Geer; Stephen H Bryant; Jeri S Roth; Jeffrey A Kowalak; Dawn M Maynard; Sanford Markey
Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry.
Journal of proteome research 2005;4(2):300-5.
2005: david 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; David Lipman; Thomas L Madden; Donna R Maglott; James Ostell; Joan U Pontius; Kim D Pruitt; Gerold Schuler; Lynn M Schriml; Edwin Sequeira; Stephen T Sherry; Karl Sirotkin; Grigory Starchenko; Tugba O Suzek; Roman L Tatusov; Tatiana Tatusova; Lukas Wagner; Eugene Yaschenko
Database resources of the National Center for Biotechnology Information.
Nucleic acids research 2005;33(Database issue):D39-45.
2005: 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; Chunlei Liu; Fu Lu; Gabriele H Marchler; Mikhail Mullokandov; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Roxanne A Yamashita; Jodie Yin; Dachuan Zhang; Stephen H Bryant
CDD: a Conserved Domain Database for protein classification.
Nucleic acids research 2005;33(Database issue):D192-6.
2004: Lewis Y Geer; Sanford Markey; Jeffrey A Kowalak; Lukas Wagner; Ming Xu; Dawn M Maynard; Xiaoyu Yang; Wenyao Shi; Stephen H Bryant
Open mass spectrometry search algorithm.
Journal of proteome research 2004;3(5):958-64.
2004: Aron Marchler-Bauer; Stephen H Bryant
CD-Search: protein domain annotations on the fly.
Nucleic acids research 2004;32(Web Server issue):W327-31.
2003: Jie Chen; John B Anderson; Carol DeWeese-Scott; Natalie Fedorova Abrams; Lewis Y Geer; Siqian He; David I Hurwitz; John D Jackson; Aviva R Jacobs; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Thomas Madej; Aron Marchler-Bauer; Gabriele H Marchler; Raja Mazumder; Anastasia N Nikolskaya; B Sridhar Rao; Anna R Panchenko; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Sona Vasudevan; Yanli Wang; Roxanne A Yamashita; Jodie Yin; Stephen H Bryant
MMDB: Entrez's 3D-structure database.
Nucleic acids research 2003;31(1):474-7.
2003: Aron Marchler-Bauer; John B Anderson; Carol DeWeese-Scott; Natalie Fedorova Abrams; Lewis Y Geer; Siqian He; David I Hurwitz; John D Jackson; Aviva R Jacobs; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Thomas Madej; Gabriele H Marchler; Raja Mazumder; Anastasia N Nikolskaya; Anna R Panchenko; B Sridhar Rao; Benjamin A Shoemaker; Vahan Simonyan; James S Song; Paul A Thiessen; Sona Vasudevan; Yanli Wang; Roxanne A Yamashita; Jodie Yin; Stephen H Bryant
CDD: a curated Entrez database of conserved domain alignments.
Nucleic acids research 2003;31(1):383-7.
2002: Lewis Y Geer; Michael Domrachev; David Lipman; Stephen H Bryant
CDART: protein homology by domain architecture.
Genome research 2002;12(10):1619-23.
2002: Aron Marchler-Bauer; Anna R Panchenko; Naomi Ariel; Stephen H Bryant
Comparison of sequence and structure alignments for protein domains.
Proteins 2002;48(3):439-46.
2002: Anna R Panchenko; Stephen H Bryant
A comparison of position-specific score matrices based on sequence and structure alignments.
Protein science : a publication of the Protein Society 2002;11(2):361-70.
2002: Aron Marchler-Bauer; Anna R Panchenko; Benjamin A Shoemaker; Paul A Thiessen; Lewis Y Geer; Stephen H Bryant
CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
Nucleic acids research 2002;30(1):281-3.
2002: 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 research 2002;30(1):249-52.
2000: Sarah J Wheelan; Aron Marchler-Bauer; Stephen H Bryant
Domain size distributions can predict domain boundaries.
Bioinformatics (Oxford, England) 2000;16(7):613-8.
2000: Y Wang; Lewis Y Geer; Colombe Chappey; JA Kans; Stephen H Bryant
Cn3D: sequence and structure views for Entrez.
Trends in biochemical sciences 2000;25(6):300-2.
2000: Anna R Panchenko; Aron Marchler-Bauer; Stephen H Bryant
Combination of threading potentials and sequence profiles improves fold recognition.
Journal of molecular biology 2000;296(5):1319-31.
2000: Yanli Wang; Kenneth J Addess; Lewis Y Geer; Thomas Madej; Aron Marchler-Bauer; D Zimmerman; Stephen H Bryant
MMDB: 3D structure data in Entrez.
Nucleic acids research 2000;28(1):243-5.
1999: Y Matsuo; Stephen H Bryant
Identification of homologous core structures.
Proteins 1999;35(1):70-9.
1999: Aron Marchler-Bauer; Stephen H Bryant
A measure of progress in fold recognition?
Proteins 1999;Suppl 3():218-25.
1999: Anna R Panchenko; Aron Marchler-Bauer; Stephen H Bryant
Threading with explicit models for evolutionary conservation of structure and sequence.
Proteins 1999;Suppl 3():133-40.
1999: Aron Marchler-Bauer; Kenneth J Addess; Colombe Chappey; Lewis Y Geer; Thomas Madej; Y Matsuo; Yanli Wang; Stephen H Bryant
MMDB: Entrez's 3D structure database.
Nucleic acids research 1999;27(1):240-3.
1997: Aron Marchler-Bauer; Stephen H Bryant
A measure of success in fold recognition.
Trends in biochemical sciences 1997;22(7):236-40.
1997: Aron Marchler-Bauer; M Levitt; Stephen H Bryant
A retrospective analysis of CASP2 threading predictions.
Proteins 1997;Suppl 1():83-91.
1997: Aron Marchler-Bauer; Stephen H Bryant
Measures of threading specificity and accuracy.
Proteins 1997;Suppl 1():74-82.
1996: Stephen H Bryant
Evaluation of threading specificity and accuracy.
Proteins 1996;26(2):172-85.
1996: C W Hogue; H Ohkawa; Stephen H Bryant
A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database.
Trends in biochemical sciences 1996;21(6):226-9.
1995: T Madej; J F Gibrat; Stephen H Bryant
Threading a database of protein cores.
Proteins 1995;23(3):356-69.
1995: T Madej; M S Boguski; Stephen H Bryant
Threading analysis suggests that the obese gene product may be a helical cytokine.
FEBS letters 1995;373(1):13-8.
1995: Andreas D Baxevanis; Stephen H Bryant; David Landsman
Homology model building of the HMG-1 box structural domain.
Nucleic acids research 1995;23(6):1019-29.
1993: Stephen H Bryant; C E Lawrence
An empirical energy function for threading protein sequence through the folding motif.
Proteins 1993;16(1):92-112.
1991: Stephen H Bryant; C E Lawrence
The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions.
Proteins 1991;9(2):108-19.