Alexander Tropsha

111 papers A* 1B 5Misc 4Journal 95Unranked 5

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2. J. Chem. Inf. Model. Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl H. Arrowsmith, Alan Ashworth, Fuqiang Ban, Hartmut Beck, Kevin P. Bishop, Hugo J. Bohórquez, Albina Bolotokova, Marko Breznik, Irene Chau, Yu Chen, Artem Cherkasov, Wim Dehaen, Dennis Della Corte, Katrin Denzinger, Niklas Piet Doering, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Francesco Gentile, Elisa Gibson, Ozan Gökdemir, Anders Gunnarsson, Judith Guenther, John J. Irwin, Jan Halborg Jensen, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Ashley Hutchinson, Shubhangi Kandwal, Andrea Karlova, Kushal Koirala, Sergei Kotelnikov, Dima Kozakov, Juyong Lee, Soowon Lee, Uta F. Lessel, Sijie Liu, Xuefeng Liu, Peter Loppnau, Jens Meiler, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Tudor I. Oprea, Brooks Paige, Amit Pandit, Keunwan Park, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Rahul Ravichandran, Didier Rognan, Edina Rosta, Yogesh Sabnis, Thomas Scott, Almagul Seitova, Purshotam Sharma, François Sindt, Minghu Song, Casper Steinmann, Rick Stevens, Valerij Talagayev, Valentyna V. Tararina, Olga O. Tarkhanova, Damon Tingey, John F. Trant, Dakota Treleaven, Alexander Tropsha, W. Patrick Walters, Jude Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Shuangjia Zheng, James S. Fraser, Matthieu Schapira
2026	J	`jnl`	GAME+: lossless knowledge-graph compression for improving the efficiency and effectiveness of rule mining. Int. J. Data Sci. Anal. Kara Schatz, Jon-Michael Beasley, Alexander Tropsha, Rada Chirkova
2026	J	`jnl`	KANEL: Kolmogorov-Arnold Network Ensemble Learning Enables Early Hit Enrichment in High-Throughput Virtual Screening. CoRR Pavel Koptev, Nikita Krainov, Konstantin Malkov, Alexander Tropsha
2025	J	`jnl`	Extending machine learning model for implicit solvation to free energy calculations. CoRR Rishabh Dey, Michael Brocidiacono, Kushal Koirala, Alexander Tropsha, Konstantin I. Popov
2025	J	`jnl`	One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening. J. Cheminformatics James Wellnitz, Sankalp Jain, Joshua E. Hochuli, Travis Maxfield, Eugene N. Muratov, Alexander Tropsha, Alexey V. Zakharov
2025	J	`jnl`	Towards Improving the Efficiency of Drug Repurposing by Leveraging Node Promiscuity in Biomedical Knowledge Graphs. ACM Trans. Comput. Heal. Daniel R. Korn, Pei-Yu Hou, Kara Schatz, Jon-Michael Beasley, Alexander Tropsha, Rada Chirkova
2024	J	`jnl`	BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. J. Chem. Inf. Model. Michael Brocidiacono, Paul G. Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha
2024	J	`jnl`	EMOE: Expansive Matching of Experts for Robust Uncertainty Based Rejection. CoRR Yunni Qu, James Wellnitz, Alexander Tropsha, Junier Oliva
2024	J	`jnl`	ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining. Bioinform. Jon-Michael Beasley, Daniel R. Korn, Nyssa N. Tucker, Erick T. M. Alves, Eugene N. Muratov, Chris Bizon, Alexander Tropsha
2024	B	`conf`	Explainable Enrichment-Driven GrAph Reasoner (EDGAR) for Large Knowledge Graphs with Applications in Drug Repurposing. IEEE Big Data Olawumi Olasunkanmi, Evan Morris, Yaphet Kebede, Harlin Lee, Stanley C. Ahalt, Alexander Tropsha, Chris Bizon
2024	J	`jnl`	Explainable Enrichment-Driven GrAph Reasoner (EDGAR) for Large Knowledge Graphs with Applications in Drug Repurposing. CoRR Olawumi Olasunkanmi, Evan Morris, Yaphet Kebede, Harlin Lee, Stanley C. Ahalt, Alexander Tropsha, Chris Bizon
2024	B	`conf`	FPP-Hunter: Expert-Guided Discovery Of Functional Path Patterns. IEEE Big Data Daniel R. Korn, Jon-Michael Beasley, Kara Schatz, Pei-Yu Hou, Alexander Tropsha, Rada Chirkova
2024	A*	`conf`	SALSA: Semantically-Aware Latent Space Autoencoder. AAAI Kathryn E. Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M. Gomez
2024	J	`jnl`	STOPLIGHT: A Hit Scoring Calculator. J. Chem. Inf. Model. James Wellnitz, Holli-Joi Martin, Mohammad Anwar Hossain, Marielle Rath, Colton Fox, Konstantin I. Popov, Timothy M. Willson, Eugene N. Muratov, Alexander Tropsha
2024	—	`conf`	Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. ECIR (2) Kathryn E. Kirchoff, James Wellnitz, Joshua E. Hochuli, Travis Maxfield, Konstantin I. Popov, Shawn M. Gomez, Alexander Tropsha
2024	J	`jnl`	Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. CoRR Kathryn E. Kirchoff, James Wellnitz, Joshua E. Hochuli, Travis Maxfield, Konstantin I. Popov, Shawn M. Gomez, Alexander Tropsha
2023	B	`conf`	GAME: Improving Efficiency and Effectiveness of Knowledge-Graph Rule Mining via Data Reduction. IEEE Big Data Kara Schatz, Alexander Tropsha, Rada Chirkova
2023	J	`jnl`	SALSA: Semantically-Aware Latent Space Autoencoder. CoRR Kathryn E. Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M. Gomez
2023	J	`jnl`	School of cheminformatics in Latin America. J. Cheminformatics Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona M. I. Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil
2022	—	`conf`	Compact Walks: Taming Knowledge-Graph Embeddings with Domain- and Task-Specific Pathways. SIGMOD Conference Pei-Yu Hou, Daniel Robert Korn, Cleber C. Melo-Filho, David R. Wright, Alexander Tropsha, Rada Chirkova
2022	J	`jnl`	The transformational role of GPU computing and deep learning in drug discovery. Nat. Mach. Intell. Mohit Pandey, Michael Fernández, Francesco Gentile, Olexandr Isayev, Alexander Tropsha, Abraham C. Stern, Artem Cherkasov
2022	Misc	`conf`	Using natural language processing to predict oral cancer risk with dental pathology notes¬¬. AMIA Malvika Pillai, Javed Mostafa, Alexander Tropsha, Amanda Seyerle, Jamie Arguello, Di Wu
2022	B	`conf`	Workflow for Domain- and Task-Sensitive Curation of Knowledge Graphs, with Use Case of DRKG. IEEE Big Data Kara Schatz, Daniel R. Korn, Alexander Tropsha, Rada Chirkova
2021	J	`jnl`	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. Daniel Robert Korn, Vera Pervitsky, Tesia M. Bobrowski, Vinicius M. Alves, Charles Schmitt, Chris Bizon, Nancy Baker, Rada Chirkova, Artem Cherkasov, Eugene N. Muratov, Alexander Tropsha
2021	J	`jnl`	COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. Bioinform. Daniel Robert Korn, Tesia M. Bobrowski, Michael Li, Yaphet Kebede, Patrick Wang, Phillips Owen, Gaurav Vaidya, Eugene N. Muratov, Rada Chirkova, Chris Bizon, Alexander Tropsha
2021	J	`jnl`	Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Comput. Biol. Zhaoping Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alexander Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan
2021	—	`conf`	Explaining Drug-Discovery Hypotheses Using Knowledge-Graph Patterns. IEEE BigData Kara Schatz, Cleber C. Melo-Filho, Alexander Tropsha, Rada Chirkova
2021	J	`jnl`	Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods. J. Chem. Inf. Model. Sankalp Jain, Vishal B. Siramshetty, Vinicius M. Alves, Eugene N. Muratov, Nicole C. Kleinstreuer, Alexander Tropsha, Marc C. Nicklaus, Anton Simeonov, Alexey V. Zakharov
2021	J	`jnl`	Learning Drug-Disease-Target Embedding (DDTE) from knowledge graphs to inform drug repurposing hypotheses. J. Biomed. Informatics Changsung Moon, Chunming Jin, Xialan Dong, Saad Mohammad Abrar, Weifan Zheng, Rada Y. Chirkova, Alexander Tropsha
2021	J	`jnl`	OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design. J. Chem. Inf. Model. Maria Korshunova, Boris Ginsburg, Alexander Tropsha, Olexandr Isayev
2021	J	`jnl`	ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database. J. Chem. Inf. Model. Tesia M. Bobrowski, Daniel Robert Korn, Eugene N. Muratov, Alexander Tropsha
2020	J	`jnl`	A semantic similarity based methodology for predicting protein-protein interactions: Evaluation with P53-interacting kinases. J. Biomed. Informatics Steven Cox, Xialan Dong, Ruhi Rai, Laura Christopherson, Weifan Zheng, Alexander Tropsha, Charles Schmitt
2020	J	`jnl`	Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
2020	J	`jnl`	Joint Virtual Special Issue on Computational Toxicology. J. Chem. Inf. Model. Igor V. Tetko, Alexander Tropsha
2020	J	`jnl`	SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules. J. Chem. Inf. Model. Vinicius M. Alves, Stephen J. Capuzzi, Rodolpho C. Braga, Daniel Robert Korn, Joshua E. Hochuli, Kyle H. Bowler, Adam Yasgar, Ganesha Rai, Anton Simeonov, Eugene N. Muratov, Alexey V. Zakharov, Alexander Tropsha
2020	J	`jnl`	Text Mining to Identify and Extract Novel Disease Treatments From Unstructured Datasets. CoRR Rahul Yedida, Saad Mohammad Abrar, Cleber C. Melo-Filho, Eugene N. Muratov, Rada Chirkova, Alexander Tropsha
2020	Misc	`conf`	Use of the Open ROBOKOP Knowledge Graph-Based Application to Provide Mechanistic Explanations for Observed Associations between Environmental Exposures and Immune-Mediated Diseases. AMIA Karamarie Fecho, Chris Bizon, Frederick W. Miller, Shepherd Schurman, Charles Schmitt, William Xue, Patrick Wang, Kenneth D. Morton, Steven Cox, Alexander Tropsha
2019	J	`jnl`	A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service. J. Am. Medical Informatics Assoc. Karamarie Fecho, Emily R. Pfaff, Hao Xu, James Champion, Steve Cox, Lisa Stillwell, David B. Peden, Chris Bizon, Ashok Kumar Krishnamurthy, Alexander Tropsha, Stanley C. Ahalt
2019	J	`jnl`	Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides. Bioinform. Sherif Farag, Rachel M. Bleich, Elizabeth A. Shank, Olexandr Isayev, Albert A. Bowers, Alexander Tropsha
2019	J	`jnl`	Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. J. Chem. Inf. Model. Michael Fernández, Fuqiang Ban, Godwin Woo, Olexandr Isayev, Carl Perez, Valery Fokin, Alexander Tropsha, Artem Cherkasov
2019	J	`jnl`	ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources. J. Chem. Inf. Model. Chris Bizon, Steven Cox, James P. Balhoff, Yaphet Kebede, Patrick Wang, Kenneth Morton, Karamarie Fecho, Alexander Tropsha
2019	J	`jnl`	ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering. Bioinform. Kenneth Morton, Patrick Wang, Chris Bizon, Steven Cox, James P. Balhoff, Yaphet Kebede, Karamarie Fecho, Alexander Tropsha
2018	J	`jnl`	Chemistry, information and Frank: a tribute to Frank Brown. J. Comput. Aided Mol. Des. Dimitris K. Agrafiotis, M. Katharine Holloway, Scott A. Johnson, Charles H. Reynolds, Terry R. Stouch, Alexander Tropsha, Chris L. Waller
2018	J	`jnl`	Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships. J. Chem. Inf. Model. Yen S. Low, Vinicius M. Alves, Denis Fourches, Alexander Sedykh, Carolina Horta Andrade, Eugene N. Muratov, Ivan Rusyn, Alexander Tropsha
2018	J	`jnl`	Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed. J. Chem. Inf. Model. Stephen J. Capuzzi, Thomas E. Thornton, Kammy Liu, Nancy Baker, Wai In Lam, Colin P. O'banion, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha
2018	J	`jnl`	Materials Informatics. J. Chem. Inf. Model. Hanoch Senderowitz, Alexander Tropsha
2018	J	`jnl`	Materials Informatics. J. Chem. Inf. Model. Hanoch Senderowitz, Alexander Tropsha
2018	J	`jnl`	Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models. J. Chem. Inf. Model. Vinicius M. Alves, Alexander Golbraikh, Stephen J. Capuzzi, Kammy Liu, Wai In Lam, Daniel Robert Korn, Diane Pozefsky, Carolina Horta Andrade, Eugene N. Muratov, Alexander Tropsha
2017	J	`jnl`	Chembench: A Publicly Accessible, Integrated Cheminformatics Portal. J. Chem. Inf. Model. Stephen J. Capuzzi, Ian Sang-June Kim, Wai In Lam, Thomas E. Thornton, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha
2017	J	`jnl`	Deep Reinforcement Learning for De-Novo Drug Design. CoRR Mariya Popova, Olexandr Isayev, Alexander Tropsha
2017	J	`jnl`	Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS. J. Chem. Inf. Model. Stephen J. Capuzzi, Eugene N. Muratov, Alexander Tropsha
2017	J	`jnl`	Pred-Skin: A Fast and Reliable Web Application to Assess Skin Sensitization Effect of Chemicals. J. Chem. Inf. Model. Rodolpho C. Braga, Vinicius M. Alves, Eugene N. Muratov, Judy Strickland, Nicole C. Kleinstreuer, Alexander Tropsha, Carolina Horta Andrade
2016	J	`jnl`	Cheminformatics-aided pharmacovigilance: application to Stevens-Johnson Syndrome. J. Am. Medical Informatics Assoc. Yen S. Low, Ola Caster, Tomas Bergvall, Denis Fourches, Xiaoling Zang, G. Niklas Norén, Ivan Rusyn, I. Ralph Edwards, Alexander Tropsha
2016	J	`jnl`	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. Regina Politi, Marino Convertino, Konstantin I. Popov, Nikolay V. Dokholyan, Alexander Tropsha
2016	J	`jnl`	Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation. J. Chem. Inf. Model. Denis Fourches, Eugene N. Muratov, Alexander Tropsha
2015	J	`jnl`	Beware of J. Chem. Inf. Model. David L. J. Alexander, Alexander Tropsha, David A. Winkler
2015	J	`jnl`	Letter from the Editors. J. Chem. Inf. Model. Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab
2015	J	`jnl`	Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark. J. Chem. Inf. Model. Denis Fourches, Regina Politi, Alexander Tropsha
2014	J	`jnl`	Application of Quantitative Structure-Activity Relationship Models of 5-HT J. Chem. Inf. Model. Man Luo, Xiang Simon Wang, Bryan L. Roth, Alexander Golbraikh, Alexander Tropsha
2014	J	`jnl`	Chemistry-wide association studies (CWAS) to determine joint toxicity effects of co-occurring chemical features. J. Cheminformatics Yen S. Low, Alexander Sedykh, Denis Fourches, Alexander Tropsha
2014	J	`jnl`	Data Set Modelability by QSAR. J. Chem. Inf. Model. Alexander Golbraikh, Eugene N. Muratov, Denis Fourches, Alexander Tropsha
2014	J	`jnl`	Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software. J. Cheminformatics Denis Fourches, Alexander Tropsha
2014	J	`jnl`	HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data. Bioinform. Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha
2013	J	`jnl`	A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth. Comput. Biol. Chem. Elebeoba E. May, Andrei Leitão, Alexander Tropsha, Tudor I. Oprea
2013	J	`jnl`	Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening. J. Chem. Inf. Model. Liying Zhang, Denis Fourches, Alexander Sedykh, Hao Zhu, Alexander Golbraikh, Sean Ekins, Julie Clark, Michele C. Connelly, Martina Sigal, Dena Hodges, Armand Guiguemde, R. Kiplin Guy, Alexander Tropsha
2013	J	`jnl`	Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. J. Chem. Inf. Model. Denis Fourches, Eugene N. Muratov, Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha
2013	—	`conf`	Semantics-driven frequent data pattern mining on electronic health records for effective adverse drug event monitoring. BIBM Jingshan Huang, Jun Huan, Alexander Tropsha, Jiangbo Dang, He Zhang, Min Xiong
2012	J	`jnl`	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. Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha
2012	J	`jnl`	Does Rational Selection of Training and Test Sets Improve the Outcome of QSAR Modeling? J. Chem. Inf. Model. Todd M. Martin, Paul Harten, Douglas M. Young, Eugene N. Muratov, Alexander Golbraikh, Hao Zhu, Alexander Tropsha
2011	J	`jnl`	Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets. J. Chem. Inf. Model. Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha
2010	J	`jnl`	Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Artem Cherkasov, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus-Robert Müller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Süleyman Cenk Sahinalp, Roberto Todeschini, Pavel G. Polishchuk, Anatoly G. Artemenko, Victor Kuzmin, Todd M. Martin, Douglas M. Young, Denis Fourches, Eugene N. Muratov, Alexander Tropsha, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexandre Varnek, Volodymyr V. Prokopenko, Igor V. Tetko
2010	J	`jnl`	Chembench: a cheminformatics workbench. Bioinform. Theo Walker, Christopher M. Grulke, Diane Pozefsky, Alexander Tropsha
2010	J	`jnl`	Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs. IEEE Trans. Inf. Technol. Biomed. Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha
2010	J	`jnl`	Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research. J. Chem. Inf. Model. Denis Fourches, Eugene N. Muratov, Alexander Tropsha
2009	J	`jnl`	Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. J. Comput. Aided Mol. Des. Deepak Bandyopadhyay, Jun Huan, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha
2009	J	`jnl`	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. Deepak Bandyopadhyay, Jun Huan, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha
2009	J	`jnl`	Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation. J. Chem. Inf. Model. Hao Tang, Xiang S. Wang, Xi-Ping Huang, Bryan L. Roth, Kyle V. Butler, Alan P. Kozikowski, Mira Jung, Alexander Tropsha
2009	—	`ch.`	QSARModeling. Encyclopedia of Complexity and Systems Science Alexander Tropsha
2008	J	`jnl`	Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. J. Chem. Inf. Model. Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko
2008	J	`jnl`	Combinatorial QSAR Modeling of Specificity and Subtype Selectivity of Ligands Binding to Serotonin Receptors 5HT1E and 5HT1F. J. Chem. Inf. Model. Xiang S. Wang, Hao Tang, Alexander Golbraikh, Alexander Tropsha
2008	J	`jnl`	Critical Assessment of QSAR Models of Environmental Toxicity against J. Chem. Inf. Model. Igor V. Tetko, Iurii Sushko, Anil Kumar Pandey, Hao Zhu, Alexander Tropsha, Ester Papa, Tomas Öberg, Roberto Todeschini, Denis Fourches, Alexandre Varnek
2008	J	`jnl`	Differentiation of AmpC beta-lactamase binders vs. decoys using classification J. Comput. Aided Mol. Des. Jui-Hua Hsieh, Xiang S. Wang, Denise G. Teotico, Alexander Golbraikh, Alexander Tropsha
2008	J	`jnl`	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. Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender, Alexander Tropsha
2008	—	`conf`	Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs. BIBM Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha
2007	J	`jnl`	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. Shuxing Zhang, Linyi Wei, Ken Bastow, Weifan Zheng, Arnold Brossi, Kuo-Hsiung Lee, Alexander Tropsha
2006	J	`jnl`	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. Shuxing Zhang, Alexander Golbraikh, Scott Oloff, Harold Kohn, Alexander Tropsha
2006	J	`jnl`	Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI). J. Chem. Inf. Model. Scott Oloff, Shuxing Zhang, Nagamani Sukumar, Curt M. Breneman, Alexander Tropsha
2006	J	`jnl`	Combinatorial QSAR Modeling of P-Glycoprotein Substrates. J. Chem. Inf. Model. Patricia de Cerqueira Lima, Alexander Golbraikh, Scott Oloff, Yunde Xiao, Alexander Tropsha
2005	J	`jnl`	Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs. J. Comput. Biol. Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan F. Prins, Alexander Tropsha
2005	J	`jnl`	Quantitative Structure-activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the J. Comput. Aided Mol. Des. José L. Medina-Franco, Alexander Golbraikh, Scott Oloff, Rafael Castillo, Alexander Tropsha
2005	Misc	`conf`	Session Introduction: Biogeometry: Applications of Computational Geometry to Molecular Structure. Pacific Symposium on Biocomputing Alexander Tropsha, Herbert Edelsbrunner
2004	Misc	`conf`	Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis. Pacific Symposium on Biocomputing Jun Huan, Wei Wang, Anglina Washington, Jan F. Prins, Ruchir Shah, Alexander Tropsha
2004	J	`jnl`	Combinatorial QSAR of Ambergris Fragrance Compounds. J. Chem. Inf. Model. Assia Kovatcheva, Alexander Golbraikh, Scott Oloff, Yun-De Xiao, Weifan Zheng, Peter Wolschann, Gerhard Buchbauer, Alexander Tropsha
2004	B	`conf`	Mining protein family specific residue packing patterns from protein structure graphs. RECOMB Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan F. Prins, Alexander Tropsha
2003	J	`jnl`	Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinform. Bala Krishnamoorthy, Alexander Tropsha
2003	J	`jnl`	QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology. J. Chem. Inf. Comput. Sci. Alexander Golbraikh, Alexander Tropsha
2003	J	`jnl`	Rational selection of training and test sets for the development of validated QSAR models. J. Comput. Aided Mol. Des. Alexander Golbraikh, Min Shen, Zhiyan Xiao, Yun-De Xiao, Kuo-Hsiung Lee, Alexander Tropsha
2002	J	`jnl`	Novel ZE-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis. J. Chem. Inf. Comput. Sci. Alexander Golbraikh, Danail Bonchev, Alexander Tropsha
2002	J	`jnl`	Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. J. Comput. Aided Mol. Des. Alexander Golbraikh, Alexander Tropsha
2001	J	`jnl`	Diversity and Coverage of Structural Sublibraries Selected Using the SAGE and SCA Algorithms. J. Chem. Inf. Comput. Sci. Charles H. Reynolds, Alexander Tropsha, Lori B. Pfahler, Ross Druker, Subhas Chakravorty, G. Ethiraj, Weifan Zheng
2001	J	`jnl`	Novel Chirality Descriptors Derived from Molecular Topology. J. Chem. Inf. Comput. Sci. Alexander Golbraikh, Danail Bonchev, Alexander Tropsha
2000	J	`jnl`	An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization. J. Chem. Inf. Comput. Sci. Dexuan Xie, Alexander Tropsha, Tamar Schlick
2000	J	`jnl`	Novel Variable Selection Quantitative Structure-Property Relationship Approach Based on the k-Nearest-Neighbor Principle. J. Chem. Inf. Comput. Sci. Weifan Zheng, Alexander Tropsha
1999	J	`jnl`	Automated Pharmacophore Identification for Large Chemical Data Sets1. J. Chem. Inf. Comput. Sci. Xin Chen, Andrew Rusinko III, Alexander Tropsha, S. Stanley Young
1999	J	`jnl`	Generalized linear response method: Application to hydration free energy calculations. J. Comput. Chem. Xin Chen, Alexander Tropsha
1999	J	`jnl`	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. Weifan Zheng, Sung Jin Cho, Chris L. Waller, Alexander Tropsha
1998	J	`jnl`	Rational Combinatorial Library Design. 1. Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries. J. Chem. Inf. Comput. Sci. Weifan Zheng, Sung Jin Cho, Alexander Tropsha
1998	J	`jnl`	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. Sung Jin Cho, Weifan Zheng, Alexander Tropsha
1996	J	`jnl`	Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues. J. Comput. Biol. Raj K. Singh, Alexander Tropsha, Iosif I. Vaisman
1995	J	`jnl`	Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer. Comput. Appl. Biosci. D. L. Hoffman, S. Laiter, Raj K. Singh, Iosif I. Vaisman, Alexander Tropsha
1994	J	`jnl`	Molecular Simulation of Alkyl Boronic Acids: Molecular Mechanics and Solvation Free Energy Calculations. J. Comput. Chem. Xiannong Chen, Libero Bartolotti, Khalid Ishaq, Alexander Tropsha