List of works - Stephen H. Bryant

A comparison of position‐specific score matrices based on sequence and structure alignments ⬇️

scientific article published on February 1, 2002

A novel method for mining highly imbalanced high-throughput screening data in PubChem

scientific article

A retrospective analysis of CASP2 threading predictions

article

A structure-based method for protein sequence alignment

scientific article

An overview of the PubChem BioAssay resource

scientific article (publication date: 2010)

Annotation of functional sites with the Conserved Domain Database

scientific article

Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space

scientific article

Automated annotation of chemical names in the literature with tunable accuracy

scientific article (publication date: 22 November 2011)

Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes

scientific article

Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection

scientific article

Biological Assembly Comparison with VAST

scientific article published on 01 January 2020

CD-Search: protein domain annotations on the fly

scientific article (publication date: July 2004)

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

scientific article

CDD: NCBI's conserved domain database

scientific article (publication date: 2015)

CDD: a Conserved Domain Database for protein classification

scientific article

CDD: a Conserved Domain Database for the functional annotation of proteins

scientific article

CDD: a conserved domain database for interactive domain family analysis

scientific article

CDD: conserved domains and protein three-dimensional structure

scientific article

CDD: specific functional annotation with the Conserved Domain Database

scientific article

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

scientific article

Characterizing protein domain associations by Small-molecule ligand binding ⬇️

scientific article published on December 3, 2012

Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem

scientific article (publication date: 2016)

Comparison of sequence and structure alignments for protein domains.

scientific article

Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex

scientific article

Database resources of the National Center for Biotechnology Information

scientific article (published 2012-01-01)

Database resources of the National Center for Biotechnology Information

scientific article

Database resources of the National Center for Biotechnology Information

scientific article (published 2010-01-01)

Database resources of the National Center for Biotechnology Information

scientific article (publication date: 2007)

Database resources of the National Center for Biotechnology Information

scientific article (published 2005-01-01)

Database resources of the National Center for Biotechnology Information

scientific article (published 2006-01-01)

Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem

scientific article

Evolution of protein binding modes in homooligomers

scientific article

Exploring functional roles of multibinding protein interfaces

scientific article

FSelector: a Ruby gem for feature selection

scientific article

Fast 3D shape screening of large chemical databases through alignment-recycling

scientific article

Finding biologically relevant protein domain interactions: conserved binding mode analysis

scientific article published on 29 December 2005

Functional specificity lies within the properties and evolutionary changes of amino acids

scientific article

Functional states of homooligomers: insights from the evolution of glycosyltransferases

scientific article

High-Throughput Screening Assay Datasets from the PubChem Database

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites ⬇️

scientific article published on January 31, 2012

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

scientific article

Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge ⬇️

scientific article published on February 9, 2012

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

scientific article

Knowledge-based annotation of small molecule binding sites in proteins

scientific article published in July 2010

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

scientific article

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

scientific article

MMDB: 3D structures and macromolecular interactions

scientific article

MMDB: Entrez's 3D-structure database

scientific article

MMDB: Entrez's 3D-structure database.

scientific article

MMDB: annotating protein sequences with Entrez's 3D-structure database

scientific article published on 29 November 2006

Measures of threading specificity and accuracy

scholarly article by Aron Marchler-Bauer published in January 1997

Modeling the evolution of protein domain architectures using maximum parsimony

scientific article published on 10 November 2006

Modulating Protein–Protein Interactions with Small Molecules: The Importance of Binding Hotspots ⬇️

scientific article published on December 16, 2011

Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors ⬇️

scientific article published on July 7, 2011

PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem

scientific article published on 30 April 2015

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 ⬇️

scientific article published on April 4, 2013

Prediction of functional sites by analysis of sequence and structure conservation

scientific article published on 9 March 2004

Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins

scientific article published on 10 April 2007

PubChem BioAssay: 2017 update

scientific article

PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing

article

PubChem Substance and Compound databases

scientific article (publication date: 4 January 2016)

PubChem applications in drug discovery: a bibliometric analysis

scientific article

PubChem as a public resource for drug discovery

scientific article (publication date: December 2010)

PubChem atom environments

scientific article (publication date: 2015)

PubChem structure–activity relationship (SAR) clusters

scientific article (publication date: 2015)

PubChem's BioAssay Database

scientific article

PubChem3D: Biologically relevant 3-D similarity

scientific article

PubChem3D: Conformer generation

scientific article (publication date: 27 January 2011)

PubChem3D: Diversity of shape

scientific article

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

scientific article

PubChem3D: Similar conformers

scientific article

PubChem3D: a new resource for scientists

scientific article

PubChem3D: conformer ensemble accuracy

scientific article

QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules

scientific article

Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets

scientific article (publication date: 4 November 2016)

Structure-based virtual screening for drug discovery: a problem-centric review

scientific article

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

scientific article

Target enhanced 2D similarity search by using explicit biological activity annotations and profiles

scientific article (publication date: 2015)

The NCBI BioSystems database

scientific article

The PubChem chemical structure sketcher

scientific article (publication date: 17 December 2009)

Threading with explicit models for evolutionary conservation of structure and sequence

scholarly article by Anna Panchenko published in January 1999

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

scientific article published on 01 January 2020

List of works by Stephen H. Bryant

A comparison of position‐specific score matrices based on sequence and structure alignments ⬇️

A novel method for mining highly imbalanced high-throughput screening data in PubChem

A retrospective analysis of CASP2 threading predictions

A structure-based method for protein sequence alignment

An overview of the PubChem BioAssay resource

Annotation of functional sites with the Conserved Domain Database

Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space

Automated annotation of chemical names in the literature with tunable accuracy

Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes

Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection

Biological Assembly Comparison with VAST

CD-Search: protein domain annotations on the fly

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

CDD: NCBI's conserved domain database

CDD: a Conserved Domain Database for protein classification

CDD: a Conserved Domain Database for the functional annotation of proteins

CDD: a conserved domain database for interactive domain family analysis

CDD: conserved domains and protein three-dimensional structure

CDD: specific functional annotation with the Conserved Domain Database

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization

Characterizing protein domain associations by Small-molecule ligand binding ⬇️

Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem

Comparison of sequence and structure alignments for protein domains.

Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Database resources of the National Center for Biotechnology Information

Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem

Evolution of protein binding modes in homooligomers

Exploring functional roles of multibinding protein interfaces

FSelector: a Ruby gem for feature selection

Fast 3D shape screening of large chemical databases through alignment-recycling

Finding biologically relevant protein domain interactions: conserved binding mode analysis

Functional specificity lies within the properties and evolutionary changes of amino acids

Functional states of homooligomers: insights from the evolution of glycosyltransferases

High-Throughput Screening Assay Datasets from the PubChem Database

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites ⬇️

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge ⬇️

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

Knowledge-based annotation of small molecule binding sites in proteins

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

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

MMDB: 3D structures and macromolecular interactions

MMDB: Entrez's 3D-structure database

MMDB: Entrez's 3D-structure database.

MMDB: annotating protein sequences with Entrez's 3D-structure database

Measures of threading specificity and accuracy

Modeling the evolution of protein domain architectures using maximum parsimony

Modulating Protein–Protein Interactions with Small Molecules: The Importance of Binding Hotspots ⬇️

Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors ⬇️

PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem

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 ⬇️

Prediction of functional sites by analysis of sequence and structure conservation

Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins

PubChem BioAssay: 2017 update

PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing

PubChem Substance and Compound databases

PubChem applications in drug discovery: a bibliometric analysis

PubChem as a public resource for drug discovery

PubChem atom environments

PubChem structure–activity relationship (SAR) clusters

PubChem's BioAssay Database

PubChem3D: Biologically relevant 3-D similarity

PubChem3D: Conformer generation

PubChem3D: Diversity of shape

PubChem3D: Shape compatibility filtering using molecular shape quadrupoles

PubChem3D: Similar conformers

PubChem3D: a new resource for scientists

PubChem3D: conformer ensemble accuracy

QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules

Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets

Structure-based virtual screening for drug discovery: a problem-centric review

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

Target enhanced 2D similarity search by using explicit biological activity annotations and profiles

The NCBI BioSystems database