Alexander Tropsha
Orcid: 0000-0003-3802-8896
According to our database1,
Alexander Tropsha
authored at least 96 papers
between 1994 and 2024.
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Bibliography
2024
J. Chem. Inf. Model., 2024
Proceedings of the Advances in Information Retrieval, 2024
Proceedings of the Thirty-Eighth AAAI Conference on Artificial Intelligence, 2024
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
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
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
Bioinform., 2021
Proceedings of the 2021 IEEE International Conference on Big Data (Big Data), 2021
2020
J. Chem. Inf. Model., 2020
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
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
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
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
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
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
J. Chem. Inf. Model., 2016
J. Am. Medical Informatics Assoc., 2016
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
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
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
2009
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
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
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
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
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
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