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2020 – today
- 2024
[j82]Michael Brocidiacono
, Paul G. Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha:
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. J. Chem. Inf. Model. 64(7): 2488-2495 (2024)- [j81]James Wellnitz, Holli-Joi Martin, Mohammad Anwar Hossain, Marielle Rath, Colton Fox, Konstantin I. Popov, Timothy M. Willson, Eugene N. Muratov, Alexander Tropsha:
STOPLIGHT: A Hit Scoring Calculator. J. Chem. Inf. Model. 64(11): 4387-4391 (2024) - [c13]Kathryn E. Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M. Gomez:
SALSA: Semantically-Aware Latent Space Autoencoder. AAAI 2024: 13211-13219 - [c12]Kathryn E. Kirchoff, James Wellnitz, Joshua E. Hochuli, Travis Maxfield, Konstantin I. Popov, Shawn M. Gomez, Alexander Tropsha:
Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. ECIR (2) 2024: 34-49 - [i6]Kathryn E. Kirchoff, James Wellnitz, Joshua E. Hochuli, Travis Maxfield, Konstantin I. Popov, Shawn M. Gomez, Alexander Tropsha:
Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. CoRR abs/2402.07970 (2024) - [i5]Yunni Qu, James Wellnitz, Alexander Tropsha, Junier Oliva:
EMOE: Expansive Matching of Experts for Robust Uncertainty Based Rejection. CoRR abs/2406.01825 (2024) - [i4]Olawumi Olasunkanmi, Evan Morris, Yaphet Kebede, Harlin Lee, Stanley C. Ahalt, Alexander Tropsha, Chris Bizon:
Explainable Enrichment-Driven GrAph Reasoner (EDGAR) for Large Knowledge Graphs with Applications in Drug Repurposing. CoRR abs/2409.18659 (2024) - 2023
- [j80]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:
School of cheminformatics in Latin America. J. Cheminformatics 15(1): 82 (2023) - [c11]Kara Schatz, Alexander Tropsha, Rada Chirkova:
GAME: Improving Efficiency and Effectiveness of Knowledge-Graph Rule Mining via Data Reduction. IEEE Big Data 2023: 4248-4257 - [i3]Kathryn E. Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M. Gomez:
SALSA: Semantically-Aware Latent Space Autoencoder. CoRR abs/2310.02744 (2023) - 2022
- [j79]Mohit Pandey, Michael Fernández, Francesco Gentile, Olexandr Isayev, Alexander Tropsha, Abraham C. Stern, Artem Cherkasov:
The transformational role of GPU computing and deep learning in drug discovery. Nat. Mach. Intell. 4(3): 211-221 (2022) - [c10]Malvika Pillai, Javed Mostafa, Alexander Tropsha, Amanda Seyerle, Jamie Arguello, Di Wu:
Using natural language processing to predict oral cancer risk with dental pathology notes¬¬. AMIA 2022 - [c9]Kara Schatz, Daniel Korn, Alexander Tropsha, Rada Chirkova:
Workflow for Domain- and Task-Sensitive Curation of Knowledge Graphs, with Use Case of DRKG. IEEE Big Data 2022: 3692-3701 - [c8]Pei-Yu Hou, Daniel Robert Korn, Cleber C. Melo-Filho, David R. Wright, Alexander Tropsha, Rada Chirkova:
Compact Walks: Taming Knowledge-Graph Embeddings with Domain- and Task-Specific Pathways. SIGMOD Conference 2022: 458-469 - 2021
- [j78]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:
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. Bioinform. 37(4): 586-587 (2021) - [j77]Changsung Moon, Chunming Jin, Xialan Dong, Saad Mohammad Abrar, Weifan Zheng, Rada Y. Chirkova, Alexander Tropsha:
Learning Drug-Disease-Target Embedding (DDTE) from knowledge graphs to inform drug repurposing hypotheses. J. Biomed. Informatics 119: 103838 (2021) - [j76]Maria Korshunova, Boris Ginsburg, Alexander Tropsha, Olexandr Isayev:
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design. J. Chem. Inf. Model. 61(1): 7-13 (2021) - [j75]Sankalp Jain, Vishal B. Siramshetty, Vinicius M. Alves, Eugene N. Muratov, Nicole C. Kleinstreuer, Alexander Tropsha, Marc C. Nicklaus, Anton Simeonov, Alexey V. Zakharov:
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods. J. Chem. Inf. Model. 61(2): 653-663 (2021) - [j74]Tesia M. Bobrowski, Daniel Robert Korn, Eugene N. Muratov, Alexander Tropsha:
ZINC Express: A Virtual Assistant for Purchasing Compounds Annotated in the ZINC Database. J. Chem. Inf. Model. 61(3): 1033-1036 (2021) - [j73]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:
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. 61(12): 5734-5741 (2021) - [c7]Kara Schatz, Cleber C. Melo-Filho, Alexander Tropsha, Rada Chirkova:
Explaining Drug-Discovery Hypotheses Using Knowledge-Graph Patterns. IEEE BigData 2021: 3709-3716 - 2020
- [j72]Steven Cox, Xialan Dong, Ruhi Rai, Laura Christopherson, Weifan Zheng, Alexander Tropsha, Charles Schmitt:
A semantic similarity based methodology for predicting protein-protein interactions: Evaluation with P53-interacting kinases. J. Biomed. Informatics 111: 103579 (2020) - [j71]Igor V. Tetko, Alexander Tropsha:
Joint Virtual Special Issue on Computational Toxicology. J. Chem. Inf. Model. 60(3): 1069-1071 (2020) - [j70]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:
SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules. J. Chem. Inf. Model. 60(8): 4056-4063 (2020) - [j69]Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang:
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 60(12): 5868-5869 (2020) - [c6]Karamarie Fecho, Chris Bizon, Frederick W. Miller, Shepherd Schurman, Charles Schmitt, William Xue, Patrick Wang, Kenneth D. Morton, Steven Cox, Alexander Tropsha:
Use of the Open ROBOKOP Knowledge Graph-Based Application to Provide Mechanistic Explanations for Observed Associations between Environmental Exposures and Immune-Mediated Diseases. AMIA 2020 - [i2]Rahul Yedida, Saad Mohammad Abrar, Cleber C. Melo-Filho, Eugene N. Muratov, Rada Chirkova, Alexander Tropsha:
Text Mining to Identify and Extract Novel Disease Treatments From Unstructured Datasets. CoRR abs/2011.07959 (2020)
2010 – 2019
- 2019
- [j68]Sherif Farag, Rachel M. Bleich, Elizabeth A. Shank, Olexandr Isayev, Albert A Bowers, Alexander Tropsha:
Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides. Bioinform. 35(19): 3584-3591 (2019) - [j67]Kenneth Morton, Patrick Wang, Chris Bizon, Steven Cox, James P. Balhoff, Yaphet Kebede, Karamarie Fecho, Alexander Tropsha:
ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering. Bioinform. 35(24): 5382-5384 (2019) - [j66]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:
A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service. J. Am. Medical Informatics Assoc. 26(10): 1064-1073 (2019) - [j65]Michael Fernández, Fuqiang Ban, Godwin Woo, Olexandr Isayev, Carl Perez, Valery Fokin, Alexander Tropsha, Artem Cherkasov:
Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. J. Chem. Inf. Model. 59(4): 1306-1313 (2019) - [j64]Chris Bizon, Steven Cox, James P. Balhoff, Yaphet Kebede, Patrick Wang, Kenneth Morton, Karamarie Fecho, Alexander Tropsha:
ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources. J. Chem. Inf. Model. 59(12): 4968-4973 (2019) - 2018
- [j63]Dimitris K. Agrafiotis, M. Katharine Holloway, Scott A. Johnson, Charles H. Reynolds, Terry R. Stouch, Alexander Tropsha, Chris L. Waller:
Chemistry, information and Frank: a tribute to Frank Brown. J. Comput. Aided Mol. Des. 32(7): 723-729 (2018) - [j62]Stephen J. Capuzzi, Thomas E. Thornton, Kammy Liu, Nancy Baker, Wai In Lam, Colin P. O'banion, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha:
Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed. J. Chem. Inf. Model. 58(2): 212-218 (2018) - [j61]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:
Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models. J. Chem. Inf. Model. 58(6): 1214-1223 (2018) - [j60]Hanoch Senderowitz, Alexander Tropsha:
Materials Informatics. J. Chem. Inf. Model. 58(7): 1313-1314 (2018) - [j59]Yen S. Low, Vinicius M. Alves, Denis Fourches, Alexander Sedykh, Carolina Horta Andrade, Eugene N. Muratov, Ivan Rusyn, Alexander Tropsha:
Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships. J. Chem. Inf. Model. 58(11): 2203-2213 (2018) - [j58]Hanoch Senderowitz, Alexander Tropsha:
Materials Informatics. J. Chem. Inf. Model. 58(12): 2377-2379 (2018) - 2017
- [j57]Stephen J. Capuzzi, Ian Sang-June Kim, Wai In Lam, Thomas E. Thornton, Eugene N. Muratov, Diane Pozefsky, Alexander Tropsha:
Chembench: A Publicly Accessible, Integrated Cheminformatics Portal. J. Chem. Inf. Model. 57(2): 105-108 (2017) - [j56]Stephen J. Capuzzi, Eugene N. Muratov, Alexander Tropsha:
Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS. J. Chem. Inf. Model. 57(3): 417-427 (2017) - [j55]Rodolpho C. Braga, Vinicius M. Alves, Eugene N. Muratov, Judy Strickland, Nicole C. Kleinstreuer, Alexander Tropsha, Carolina Horta Andrade:
Pred-Skin: A Fast and Reliable Web Application to Assess Skin Sensitization Effect of Chemicals. J. Chem. Inf. Model. 57(5): 1013-1017 (2017) - [i1]Mariya Popova, Olexandr Isayev, Alexander Tropsha:
Deep Reinforcement Learning for De-Novo Drug Design. CoRR abs/1711.10907 (2017) - 2016
- [j54]Yen S. Low, Ola Caster, Tomas Bergvall, Denis Fourches, Xiaoling Zang, G. Niklas Norén, Ivan Rusyn, I. Ralph Edwards, Alexander Tropsha:
Cheminformatics-aided pharmacovigilance: application to Stevens-Johnson Syndrome. J. Am. Medical Informatics Assoc. 23(5): 968-978 (2016) - [j53]Regina Politi, Marino Convertino, Konstantin I. Popov, Nikolay V. Dokholyan, Alexander Tropsha:
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. 56(6): 1032-1041 (2016) - [j52]Denis Fourches, Eugene N. Muratov, Alexander Tropsha:
Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation. J. Chem. Inf. Model. 56(7): 1243-1252 (2016) - 2015
- [j51]Denis Fourches, Regina Politi, Alexander Tropsha:
Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark. J. Chem. Inf. Model. 55(1): 63-71 (2015) - [j50]Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab:
Letter from the Editors. J. Chem. Inf. Model. 55(4): 719-720 (2015) - [j49]David L. J. Alexander, Alexander Tropsha, David A. Winkler:
Beware of R2: Simple, Unambiguous Assessment of the Prediction Accuracy of QSAR and QSPR Models. J. Chem. Inf. Model. 55(7): 1316-1322 (2015) - 2014
- [j48]Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha:
HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data. Bioinform. 30(4): 588-589 (2014) - [j47]Denis Fourches, Alexander Tropsha:
Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software. J. Cheminformatics 6(S-1): 14 (2014) - [j46]Yen S. Low, Alexander Sedykh, Denis Fourches, Alexander Tropsha:
Chemistry-wide association studies (CWAS) to determine joint toxicity effects of co-occurring chemical features. J. Cheminformatics 6(S-1): 15 (2014) - [j45]Alexander Golbraikh, Eugene N. Muratov, Denis Fourches, Alexander Tropsha:
Data Set Modelability by QSAR. J. Chem. Inf. Model. 54(1): 1-4 (2014) - [j44]Man Luo, Xiang Simon Wang, Bryan L. Roth, Alexander Golbraikh, Alexander Tropsha:
Application of Quantitative Structure-Activity Relationship Models of 5-HT1A Receptor Binding to Virtual Screening Identifies Novel and Potent 5-HT1A Ligands. J. Chem. Inf. Model. 54(2): 634-647 (2014) - 2013
- [j43]Elebeoba E. May, Andrei Leitão, Alexander Tropsha, Tudor I. Oprea:
A systems chemical biology study of malate synthase and isocitrate lyase inhibition in Mycobacterium tuberculosis during active and NRP growth. Comput. Biol. Chem. 47: 167-180 (2013) - [j42]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:
Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening. J. Chem. Inf. Model. 53(2): 475-492 (2013) - [j41]Denis Fourches, Eugene N. Muratov, Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha:
Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches. J. Chem. Inf. Model. 53(8): 1915-1922 (2013) - [c5]Jingshan Huang, Jun Huan, Alexander Tropsha, Jiangbo Dang, He Zhang, Min Xiong:
Semantics-driven frequent data pattern mining on electronic health records for effective adverse drug event monitoring. BIBM 2013: 608-611 - 2012
- [j40]Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha:
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. 52(1): 16-28 (2012) - [j39]Todd Martin, Paul Harten, Douglas M. Young, Eugene N. Muratov, Alexander Golbraikh, Hao Zhu, Alexander Tropsha:
Does Rational Selection of Training and Test Sets Improve the Outcome of QSAR Modeling? J. Chem. Inf. Model. 52(10): 2570-2578 (2012) - 2011
- [j38]Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha:
Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets. J. Chem. Inf. Model. 51(9): 2027-2035 (2011) - 2010
- [j37]Theo Walker, Christopher M. Grulke, Diane Pozefsky, Alexander Tropsha:
Chembench: a cheminformatics workbench. Bioinform. 26(23): 3000-3001 (2010) - [j36]Denis Fourches, Eugene N. Muratov, Alexander Tropsha:
Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research. J. Chem. Inf. Model. 50(7): 1189-1204 (2010) - [j35]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 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:
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. 50(12): 2094-2111 (2010) - [j34]Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs. IEEE Trans. Inf. Technol. Biomed. 14(5): 1137-1143 (2010)
2000 – 2009
- 2009
- [j33]Deepak Bandyopadhyay, Jun Huan, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. J. Comput. Aided Mol. Des. 23(11): 773-784 (2009) - [j32]Deepak Bandyopadhyay, Jun Huan, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
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. 23(11): 785-797 (2009) - [j31]Hao Tang, Xiang S. Wang, Xi-Ping Huang, Bryan L. Roth, Kyle V. Butler, Alan P. Kozikowski, Mira Jung, Alexander Tropsha:
Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation. J. Chem. Inf. Model. 49(2): 461-476 (2009) - [r1]Alexander Tropsha:
QSARModeling. Encyclopedia of Complexity and Systems Science 2009: 7071-7088 - 2008
- [j30]Jui-Hua Hsieh, Xiang S. Wang, Denise G. Teotico, Alexander Golbraikh, Alexander Tropsha:
Differentiation of AmpC beta-lactamase binders vs. decoys using classification k NN QSAR modeling and application of the QSAR classifier to virtual screening. J. Comput. Aided Mol. Des. 22(9): 593-609 (2008) - [j29]Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender, Alexander Tropsha:
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. 48(4): 691-703 (2008) - [j28]Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko:
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. J. Chem. Inf. Model. 48(4): 766-784 (2008) - [j27]Xiang S. Wang, Hao Tang, Alexander Golbraikh, Alexander Tropsha:
Combinatorial QSAR Modeling of Specificity and Subtype Selectivity of Ligands Binding to Serotonin Receptors 5HT1E and 5HT1F. J. Chem. Inf. Model. 48(5): 997-1013 (2008) - [j26]Igor V. Tetko, Iurii Sushko, Anil Kumar Pandey, Hao Zhu, Alexander Tropsha, Ester Papa, Tomas Öberg, Roberto Todeschini, Denis Fourches, Alexandre Varnek:
Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection. J. Chem. Inf. Model. 48(9): 1733-1746 (2008) - [c4]Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan F. Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha:
Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs. BIBM 2008: 199-206 - 2007
- [j25]Shuxing Zhang, Linyi Wei, Ken Bastow, Weifan Zheng, Arnold Brossi, Kuo-Hsiung Lee, Alexander Tropsha:
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. 21(1-3): 97-112 (2007) - 2006
- [j24]Scott Oloff, Shuxing Zhang, Nagamani Sukumar, Curt M. Breneman, Alexander Tropsha:
Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI). J. Chem. Inf. Model. 46(2): 844-851 (2006) - [j23]Patricia de Cerqueira Lima, Alexander Golbraikh, Scott Oloff, Yunde Xiao, Alexander Tropsha:
Combinatorial QSAR Modeling of P-Glycoprotein Substrates. J. Chem. Inf. Model. 46(3): 1245-1254 (2006) - [j22]Shuxing Zhang, Alexander Golbraikh, Scott Oloff, Harold Kohn, Alexander Tropsha:
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. 46(5): 1984-1995 (2006) - 2005
- [j21]José L. Medina-Franco, Alexander Golbraikh, Scott Oloff, Rafael Castillo, Alexander Tropsha:
Quantitative Structure-activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the k Nearest Neighbor Method and QSAR-based Database Mining. J. Comput. Aided Mol. Des. 19(4): 229-242 (2005) - [j20]Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan F. Prins, Alexander Tropsha:
Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs. J. Comput. Biol. 12(6): 657-671 (2005) - [j19]Peter Itskowitz, Alexander Tropsha:
k Nearest Neighbors QSAR Modeling as a Variational Problem: Theory and Applications. J. Chem. Inf. Model. 45(3): 777-785 (2005) - [c3]Alexander Tropsha, Herbert Edelsbrunner:
Session Introduction: Biogeometry: Applications of Computational Geometry to Molecular Structure. Pacific Symposium on Biocomputing 2005: 3-4 - 2004
- [j18]Assia Kovatcheva, Alexander Golbraikh, Scott Oloff, Yun-De Xiao, Weifan Zheng, Peter Wolschann, Gerhard Buchbauer, Alexander Tropsha:
Combinatorial QSAR of Ambergris Fragrance Compounds. J. Chem. Inf. Model. 44(2): 582-595 (2004) - [c2]Jun Huan, Wei Wang, Anglina Washington, Jan F. Prins, Ruchir Shah, Alexander Tropsha:
Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis. Pacific Symposium on Biocomputing 2004: 411-422 - [c1]Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan F. Prins, Alexander Tropsha:
Mining protein family specific residue packing patterns from protein structure graphs. RECOMB 2004: 308-315 - 2003
- [j17]Bala Krishnamoorthy, Alexander Tropsha:
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinform. 19(12): 1540-1548 (2003) - [j16]Alexander Golbraikh, Min Shen, Zhiyan Xiao, Yun-De Xiao, Kuo-Hsiung Lee, Alexander Tropsha:
Rational selection of training and test sets for the development of validated QSAR models. J. Comput. Aided Mol. Des. 17(2-4): 241-253 (2003) - [j15]Alexander Golbraikh, Alexander Tropsha:
QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology. J. Chem. Inf. Comput. Sci. 43(1): 144-154 (2003) - 2002
- [j14]Alexander Golbraikh, Alexander Tropsha:
Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. J. Comput. Aided Mol. Des. 16(5-6): 357-369 (2002) - [j13]Alexander Golbraikh, Danail Bonchev, Alexander Tropsha:
Novel ZE-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis. J. Chem. Inf. Comput. Sci. 42(4): 769-787 (2002) - 2001
- [j12]Alexander Golbraikh, Danail Bonchev, Alexander Tropsha:
Novel Chirality Descriptors Derived from Molecular Topology. J. Chem. Inf. Comput. Sci. 41(1): 147-158 (2001) - [j11]Charles H. Reynolds, Alexander Tropsha, Lori B. Pfahler, Ross Druker, Subhas Chakravorty, G. Ethiraj, Weifan Zheng:
Diversity and Coverage of Structural Sublibraries Selected Using the SAGE and SCA Algorithms. J. Chem. Inf. Comput. Sci. 41(6): 1470-1477 (2001) - 2000
- [j10]Dexuan Xie, Alexander Tropsha, Tamar Schlick:
An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization. J. Chem. Inf. Comput. Sci. 40(1): 167-177 (2000) - [j9]Weifan Zheng, Alexander Tropsha:
Novel Variable Selection Quantitative Structure-Property Relationship Approach Based on the k-Nearest-Neighbor Principle. J. Chem. Inf. Comput. Sci. 40(1): 185-194 (2000)
1990 – 1999
- 1999
- [j8]Xin Chen, Alexander Tropsha:
Generalized linear response method: Application to hydration free energy calculations. J. Comput. Chem. 20(8): 749-759 (1999) - [j7]Weifan Zheng, Sung Jin Cho, Chris L. Waller, Alexander Tropsha:
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. 39(4): 738-746 (1999) - [j6]Xin Chen, Andrew Rusinko III, Alexander Tropsha, S. Stanley Young:
Automated Pharmacophore Identification for Large Chemical Data Sets1. J. Chem. Inf. Comput. Sci. 39(5): 887-896 (1999) - 1998
- [j5]Weifan Zheng, Sung Jin Cho, Alexander Tropsha:
Rational Combinatorial Library Design. 1. Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries. J. Chem. Inf. Comput. Sci. 38(2): 251-258 (1998) - [j4]Sung Jin Cho, Weifan Zheng, Alexander Tropsha:
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. 38(2): 259-268 (1998) - 1996
- [j3]Raj K. Singh, Alexander Tropsha, Iosif I. Vaisman:
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