Alexander Tropsha

Orcid: 0000-0003-3802-8896

According to our database1, Alexander Tropsha authored at least 99 papers between 1994 and 2024.

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Bibliography

2024
STOPLIGHT: A Hit Scoring Calculator.
J. Chem. Inf. Model., 2024

BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening.
J. Chem. Inf. Model., 2024

Explainable Enrichment-Driven GrAph Reasoner (EDGAR) for Large Knowledge Graphs with Applications in Drug Repurposing.
CoRR, 2024

EMOE: Expansive Matching of Experts for Robust Uncertainty Based Rejection.
CoRR, 2024

Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search.
Proceedings of the Advances in Information Retrieval, 2024

SALSA: Semantically-Aware Latent Space Autoencoder.
Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024

2023
School of cheminformatics in Latin America.
J. Cheminformatics, December, 2023

GAME: Improving Efficiency and Effectiveness of Knowledge-Graph Rule Mining via Data Reduction.
Proceedings of the IEEE International Conference on Big Data, 2023

2022
The transformational role of GPU computing and deep learning in drug discovery.
Nat. Mach. Intell., 2022

Compact Walks: Taming Knowledge-Graph Embeddings with Domain- and Task-Specific Pathways.
Proceedings of the SIGMOD '22: International Conference on Management of Data, Philadelphia, PA, USA, June 12, 2022

Workflow for Domain- and Task-Sensitive Curation of Knowledge Graphs, with Use Case of DRKG.
Proceedings of the IEEE International Conference on Big Data, 2022

Using natural language processing to predict oral cancer risk with dental pathology notes¬¬.
Proceedings of the AMIA 2022, 2022

2021
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design.
J. Chem. Inf. Model., 2021

COVID-19 Knowledge Extractor (COKE): A Curated Repository of Drug-Target Associations Extracted from the CORD-19 Corpus of Scientific Publications on COVID-19.
J. Chem. Inf. Model., 2021

Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods.
J. Chem. Inf. Model., 2021

ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database.
J. Chem. Inf. Model., 2021

Learning Drug-Disease-Target Embedding (DDTE) from knowledge graphs to inform drug repurposing hypotheses.
J. Biomed. Informatics, 2021

COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database.
Bioinform., 2021

Explaining Drug-Discovery Hypotheses Using Knowledge-Graph Patterns.
Proceedings of the 2021 IEEE International Conference on Big Data (Big Data), 2021

2020
Joint Virtual Special Issue on Computational Toxicology.
J. Chem. Inf. Model., 2020

Editorial: Method and Data Sharing and Reproducibility of Scientific Results.
J. Chem. Inf. Model., 2020

SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules.
J. Chem. Inf. Model., 2020

A semantic similarity based methodology for predicting protein-protein interactions: Evaluation with P53-interacting kinases.
J. Biomed. Informatics, 2020

Text Mining to Identify and Extract Novel Disease Treatments From Unstructured Datasets.
CoRR, 2020

Use of the Open ROBOKOP Knowledge Graph-Based Application to Provide Mechanistic Explanations for Observed Associations between Environmental Exposures and Immune-Mediated Diseases.
Proceedings of the AMIA 2020, 2020

2019
Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects.
J. Chem. Inf. Model., 2019

ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources.
J. Chem. Inf. Model., 2019

A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service.
J. Am. Medical Informatics Assoc., 2019

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.
Bioinform., 2019

Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides.
Bioinform., 2019

2018
Materials Informatics.
J. Chem. Inf. Model., 2018

Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships.
J. Chem. Inf. Model., 2018

Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.
J. Chem. Inf. Model., 2018

Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models.
J. Chem. Inf. Model., 2018

Chemistry, information and Frank: a tribute to Frank Brown.
J. Comput. Aided Mol. Des., 2018

2017
Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS.
J. Chem. Inf. Model., 2017

Chembench: A Publicly Accessible, Integrated Cheminformatics Portal.
J. Chem. Inf. Model., 2017

Pred-Skin: A Fast and Reliable Web Application to Assess Skin Sensitization Effect of Chemicals.
J. Chem. Inf. Model., 2017

Deep Reinforcement Learning for De-Novo Drug Design.
CoRR, 2017

2016
Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise.
J. Chem. Inf. Model., 2016

Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation.
J. Chem. Inf. Model., 2016

Cheminformatics-aided pharmacovigilance: application to Stevens-Johnson Syndrome.
J. Am. Medical Informatics Assoc., 2016

2015
Letter from the Editors.
J. Chem. Inf. Model., 2015

Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark.
J. Chem. Inf. Model., 2015

Beware of <i>R</i><sup>2</sup>: Simple, Unambiguous Assessment of the Prediction Accuracy of QSAR and QSPR Models.
J. Chem. Inf. Model., 2015

2014
Application of Quantitative Structure-Activity Relationship Models of 5-HT<sub>1A</sub> Receptor Binding to Virtual Screening Identifies Novel and Potent 5-HT<sub>1A</sub> Ligands.
J. Chem. Inf. Model., 2014

Data Set Modelability by QSAR.
J. Chem. Inf. Model., 2014

Chemistry-wide association studies (CWAS) to determine joint toxicity effects of co-occurring chemical features.
J. Cheminformatics, 2014

Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software.
J. Cheminformatics, 2014

HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data.
Bioinform., 2014

2013
Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening.
J. Chem. Inf. Model., 2013

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches.
J. Chem. Inf. Model., 2013

A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth.
Comput. Biol. Chem., 2013

Semantics-driven frequent data pattern mining on electronic health records for effective adverse drug event monitoring.
Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012
Does Rational Selection of Training and Test Sets Improve the Outcome of QSAR Modeling?
J. Chem. Inf. Model., 2012

Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening.
J. Chem. Inf. Model., 2012

2011
Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets.
J. Chem. Inf. Model., 2011

2010
Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs.
IEEE Trans. Inf. Technol. Biomed., 2010

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set.
J. Chem. Inf. Model., 2010

Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research.
J. Chem. Inf. Model., 2010

Chembench: a cheminformatics workbench.
Bioinform., 2010

2009
QSARModeling.
Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation.
J. Chem. Inf. Model., 2009

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications.
J. Comput. Aided Mol. Des., 2009

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.
J. Comput. Aided Mol. Des., 2009

2008
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis.
J. Chem. Inf. Model., 2008

Combinatorial QSAR Modeling of Specificity and Subtype Selectivity of Ligands Binding to Serotonin Receptors 5HT1E and 5HT1F.
J. Chem. Inf. Model., 2008

Critical Assessment of QSAR Models of Environmental Toxicity against <i>Tetrahymena pyriformis: </i> Focusing on Applicability Domain and Overfitting by Variable Selection.
J. Chem. Inf. Model., 2008

Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem.
J. Chem. Inf. Model., 2008

Differentiation of AmpC beta-lactamase binders vs. decoys using classification <i>k</i> NN QSAR modeling and application of the QSAR classifier to virtual screening.
J. Comput. Aided Mol. Des., 2008

Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

2007
Antitumor Agents 252. Application of validated QSAR models to database mining: discovery of novel tylophorine derivatives as potential anticancer agents.
J. Comput. Aided Mol. Des., 2007

2006
A Novel Automated Lazy Learning QSAR (ALL-QSAR) Approach: Method Development, Applications, and Virtual Screening of Chemical Databases Using Validated ALL-QSAR Models.
J. Chem. Inf. Model., 2006

Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI).
J. Chem. Inf. Model., 2006

Combinatorial QSAR Modeling of P-Glycoprotein Substrates.
J. Chem. Inf. Model., 2006

2005
<i>k</i> Nearest Neighbors QSAR Modeling as a Variational Problem: Theory and Applications.
J. Chem. Inf. Model., 2005

Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs.
J. Comput. Biol., 2005

Quantitative Structure-activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the <i>k</i> Nearest Neighbor Method and QSAR-based Database Mining.
J. Comput. Aided Mol. Des., 2005

Session Introduction: Biogeometry: Applications of Computational Geometry to Molecular Structure.
Proceedings of the Biocomputing 2005, 2005

2004
Combinatorial QSAR of Ambergris Fragrance Compounds.
J. Chem. Inf. Model., 2004

Mining protein family specific residue packing patterns from protein structure graphs.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis.
Proceedings of the Biocomputing 2004, 2004

2003
QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology.
J. Chem. Inf. Comput. Sci., 2003

Rational selection of training and test sets for the development of validated QSAR models.
J. Comput. Aided Mol. Des., 2003

Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations.
Bioinform., 2003

2002
Novel ZE-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis.
J. Chem. Inf. Comput. Sci., 2002

Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection.
J. Comput. Aided Mol. Des., 2002

2001
Diversity and Coverage of Structural Sublibraries Selected Using the SAGE and SCA Algorithms.
J. Chem. Inf. Comput. Sci., 2001

Novel Chirality Descriptors Derived from Molecular Topology.
J. Chem. Inf. Comput. Sci., 2001

2000
Novel Variable Selection Quantitative Structure-Property Relationship Approach Based on the k-Nearest-Neighbor Principle.
J. Chem. Inf. Comput. Sci., 2000

An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization.
J. Chem. Inf. Comput. Sci., 2000

1999
Rational Combinatorial Library Design. 3. Simulated Annealing Guided Evaluation (SAGE) of Molecular Diversity: A Novel Computational Tool for Universal Library Design and Database Mining.
J. Chem. Inf. Comput. Sci., 1999

Automated Pharmacophore Identification for Large Chemical Data Sets1.
J. Chem. Inf. Comput. Sci., 1999

Generalized linear response method: Application to hydration free energy calculations.
J. Comput. Chem., 1999

1998
Rational Combinatorial Library Design. 1. Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries.
J. Chem. Inf. Comput. Sci., 1998

Rational Combinatorial Library Design. 2. Rational Design of Targeted Combinatorial Peptide Libraries Using Chemical Similarity Probe and the Inverse QSAR Approaches.
J. Chem. Inf. Comput. Sci., 1998

1996
Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues.
J. Comput. Biol., 1996

1995
Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer.
Comput. Appl. Biosci., 1995

1994
Molecular Simulation of Alkyl Boronic Acids: Molecular Mechanics and Solvation Free Energy Calculations.
J. Comput. Chem., 1994


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