Works by Tropsha, Alexander

Results: 86

Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions.

Published in:

2018

By:

La, Mary K.;
Sedykh, Alexander;
Fourches, Denis;
Muratov, Eugene;
Tropsha, Alexander

Publication type:

journal article

Making sense from antisense: A review of experimental data and developing ideas on sense-antisense peptide recognition.

Published in:

Journal of Molecular Recognition, 1992, v. 5, n. 2, p. 43, doi. 10.1002/jmr.300050202

By:

Tropsha, Alexander;
Kizer, John S.;
Chaiken, Irwin M.

Publication type:

Article

A data science roadmap for open science organizations engaged in early-stage drug discovery.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49777-x

By:

Edfeldt, Kristina;
Edwards, Aled M.;
Engkvist, Ola;
Günther, Judith;
Hartley, Matthew;
Hulcoop, David G.;
Leach, Andrew R.;
Marsden, Brian D.;
Menge, Amelie;
Misquitta, Leonie;
Müller, Susanne;
Owen, Dafydd R.;
Schütt, Kristof T.;
Skelton, Nicholas;
Steffen, Andreas;
Tropsha, Alexander;
Vernet, Erik;
Wang, Yanli;
Wellnitz, James;
Willson, Timothy M.

Publication type:

Article

HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra‐large chemical libraries.

Published in:

Molecular Informatics, 2024, v. 43, n. 1, p. 1, doi. 10.1002/minf.202300207

By:

Popov, Konstantin I.;
Wellnitz, James;
Maxfield, Travis;
Tropsha, Alexander

Publication type:

Article

Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein‐ligand Complexes.

Published in:

Molecular Informatics, 2022, v. 41, n. 8, p. 1, doi. 10.1002/minf.202100248

By:

Khashan, Raed;
Tropsha, Alexander;
Zheng, Weifan

Publication type:

Article

QSAR Modeling of SARS‐CoV M<sup>pro</sup> Inhibitors Identifies Sufugolix, Cenicriviroc, Proglumetacin, and other Drugs as Candidates for Repurposing against SARS‐CoV‐2.

Published in:

Molecular Informatics, 2021, v. 40, n. 1, p. 1, doi. 10.1002/minf.202000113

By:

Alves, Vinicius M.;
Bobrowski, Tesia;
Melo‐Filho, Cleber C.;
Korn, Daniel;
Auerbach, Scott;
Schmitt, Charles;
Muratov, Eugene N.;
Tropsha, Alexander

Publication type:

Article

Public (Q)SAR Services, Integrated Modeling Environments, and Model Repositories on the Web: State of the Art and Perspectives for Future Development.

Published in:

Molecular Informatics, 2017, v. 36, n. 3, p. n/a, doi. 10.1002/minf.201600082

By:

Tetko, Igor V.;
Maran, Uko;
Tropsha, Alexander

Publication type:

Article

Comparative Analysis of QSAR-based vs. Chemical Similarity Based Predictors of GPCRs Binding Affinity.

Published in:

Molecular Informatics, 2016, v. 35, n. 1, p. 36, doi. 10.1002/minf.201500038

By:

Luo, Man;
Wang, Xiang S.;
Tropsha, Alexander

Publication type:

Article

Drug Side Effect Profiles as Molecular Descriptors for Predictive Modeling of Target Bioactivity.

Published in:

Molecular Informatics, 2015, v. 34, n. 2/3, p. 160, doi. 10.1002/minf.201400134

By:

Baker, Nancy C.;
Fourches, DENis;
Tropsha, Alexander

Publication type:

Article

Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity.

Published in:

2015

By:

Braga, Rodolpho C.;
Alves, Vinicius M.;
Silva, Meryck F. B.;
Muratov, Eugene;
Fourches, Denis;
Lião, Luciano M.;
Tropsha, Alexander;
Andrade, Carolina H.

Publication type:

Other

The Development of Novel Chemical Fragment-Based Descriptors Using Frequent Common Subgraph Mining Approach and Their Application in QSAR Modeling.

Published in:

Molecular Informatics, 2014, v. 33, n. 3, p. 201, doi. 10.1002/minf.201300165

By:

Khashan, Raed;
Zheng, Weifan;
Tropsha, Alexander

Publication type:

Article

Using Graph Indices for the Analysis and Comparison of Chemical Datasets.

Published in:

Molecular Informatics, 2013, v. 32, n. 9/10, p. 827, doi. 10.1002/minf.201300076

By:

Fourches, Denis;
Tropsha, Alexander

Publication type:

Article

Best Practices for QSAR Model Development, Validation, and Exploitation.

Published in:

Molecular Informatics, 2010, v. 29, n. 6/7, p. 476, doi. 10.1002/minf.201000061

By:

Tropsha, Alexander

Publication type:

Article

Activity prediction and identification of mis-annotated chemical compounds using extreme descriptors.

Published in:

Journal of Chemometrics, 2016, v. 30, n. 3, p. 99, doi. 10.1002/cem.2776

By:

Borysov, Petro;
Hannig, Jan;
Marron, J. S.;
Muratov, Eugene;
Fourches, Denis;
Tropsha, Alexander

Publication type:

Article

ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining.

Published in:

2024

By:

Beasley, Jon-Michael T;
Korn, Daniel R;
Tucker, Nyssa N;
Alves, Erick T M;
Muratov, Eugene N;
Bizon, Chris;
Tropsha, Alexander

Publication type:

Case Study

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

Published in:

Bioinformatics, 2021, v. 37, n. 4, p. 586, doi. 10.1093/bioinformatics/btaa718

By:

Korn, Daniel;
Bobrowski, Tesia;
Li, Michael;
Kebede, Yaphet;
Wang, Patrick;
Owen, Phillips;
Vaidya, Gaurav;
Muratov, Eugene;
Chirkova, Rada;
Bizon, Chris;
Tropsha, Alexander

Publication type:

Article

Modernization of Enoxaparin Molecular Weight Determination Using Homogeneous Standards.

Published in:

Pharmaceuticals (14248247), 2017, v. 10, n. 3, p. 66, doi. 10.3390/ph10030066

By:

Arnold, Katelyn M.;
Capuzzi, Stephen J.;
Yongmei Xu;
Muratov, Eugene N.;
Carrick, Kevin;
Szajek, Anita Y.;
Tropsha, Alexander;
Jian Liu

Publication type:

Article

School of cheminformatics in Latin America.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00758-0

By:

Gonzalez-Ponce, Karla;
Horta Andrade, Carolina;
Hunter, Fiona;
Kirchmair, Johannes;
Martinez-Mayorga, Karina;
Medina-Franco, José L.;
Rarey, Matthias;
Tropsha, Alexander;
Varnek, Alexandre;
Zdrazil, Barbara

Publication type:

Article

Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.

Published in:

Proteins, 2004, v. 56, n. 4, p. 828, doi. 10.1002/prot.20131

By:

Sherman, Douglas B.;
Zhang, Shuxing;
Pitner, J. Bruce;
Tropsha, Alexander

Publication type:

Article

Lattice protein folding with two and four-body statistical potentials.

Published in:

Proteins, 2001, v. 43, n. 2, p. 161, doi. 10.1002/1097-0134(20010501)43:2<161::AID-PROT1028>3.0.CO;2-F

By:

Gan, Hin Hark;
Tropsha, Alexander;
Schlick, Tamar

Publication type:

Article

The 'random-coil' state of proteins: Comparison of database statistics and molecular simulations.

Published in:

Proteins, 1999, v. 36, n. 4, p. 407, doi. 10.1002/(SICI)1097-0134(19990901)36:4<407::AID-PROT4>3.0.CO;2-1

By:

O'Connell, Thomas M.;
Wang, Lu;
Tropsha, Alexander;
Hermans, Jan

Publication type:

Article

Shedding the Light on Post-Vaccine Myocarditis and Pericarditis in COVID-19 and Non-COVID-19 Vaccine Recipients.

Published in:

Vaccines, 2021, v. 9, n. 10, p. 1186, doi. 10.3390/vaccines9101186

By:

Hajjo, Rima;
Sabbah, Dima A.;
Bardaweel, Sanaa K.;
Tropsha, Alexander

Publication type:

Article

A Novel Machine Learning Model and a Web Portal for Predicting the Human Skin Sensitization Effects of Chemical Agents.

Published in:

Toxics, 2024, v. 12, n. 11, p. 803, doi. 10.3390/toxics12110803

By:

Scheufen Tieghi, Ricardo;
Moreira-Filho, José Teófilo;
Martin, Holli-Joi;
Wellnitz, James;
Otoch, Miguel Canamary;
Rath, Marielle;
Tropsha, Alexander;
Muratov, Eugene N.;
Kleinstreuer, Nicole

Publication type:

Article

Generalized linear response method: Application to hydration free energy calculations.

Published in:

Journal of Computational Chemistry, 1999, v. 20, n. 8, p. 749, doi. 10.1002/(SICI)1096-987X(199906)20:8<749::AID-JCC1>3.0.CO;2-I

By:

Chen, Xin;
Tropsha, Alexander

Publication type:

Article

Molecular simulation of alkyl boronic acids: Molecular mechanics and solvation free energy calculations.

Published in:

Journal of Computational Chemistry, 1994, v. 15, n. 3, p. 333, doi. 10.1002/jcc.540150308

By:

Chen, Xiannong;
Bartolotti, Libero;
Ishaq, Khalid;
Tropsha, Alexander

Publication type:

Article

Chemistry, information and Frank: a tribute to Frank Brown.

Published in:

2018

By:

Agrafiotis, Dimitris K.;
Holloway, M. Katharine;
Johnson, Scott Arne;
Reynolds, Charles H.;
Stouch, Terry Richard;
Tropsha, Alexander;
Waller, Chris L.

Publication type:

Obituary

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.

Published in:

Journal of Computer-Aided Molecular Design, 2009, v. 23, n. 11, p. 773, doi. 10.1007/s10822-009-9273-4

By:

Bandyopadhyay, Deepak;
Jun Huan;
Prins, Jan;
Snoeyink, Jack;
Wei Wang;
Tropsha, Alexander

Publication type:

Article

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications.

Published in:

Journal of Computer-Aided Molecular Design, 2009, v. 23, n. 11, p. 785, doi. 10.1007/s10822-009-9277-0

By:

Bandyopadhyay, Deepak;
Jun Huan;
Prins, Jan;
Snoeyink, Jack;
Wei Wang;
Tropsha, Alexander

Publication type:

Article

Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening.

Published in:

Journal of Computer-Aided Molecular Design, 2008, v. 22, n. 9, p. 593, doi. 10.1007/s10822-008-9199-2

By:

Jui-Hua Hsieh;
Xiang Wang;
Teotico, Denise;
Golbraikh, Alexander;
Tropsha, Alexander

Publication type:

Article

Antitumor Agents 252. Application of validated QSAR models to database mining: discovery of novel tylophorine derivatives as potential anticancer agents.

Published in:

Journal of Computer-Aided Molecular Design, 2007, v. 21, n. 1-3, p. 97, doi. 10.1007/s10822-007-9102-6

By:

Shuxing Zhang;
Linyi Wei;
Bastow, Ken;
Weifan Zheng;
Brossi, Arnold;
Kuo-Hsiung Lee;
Tropsha, Alexander

Publication type:

Article

Quantitative Structure–activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the k Nearest Neighbor Method and QSAR-based Database Mining.

Published in:

Journal of Computer-Aided Molecular Design, 2005, v. 19, n. 4, p. 229, doi. 10.1007/s10822-005-4789-8

By:

Medina-Franco, Jose Luis;
Golbraikh, Alexander;
Oloff, Scott;
Castillo, Rafael;
Tropsha, Alexander

Publication type:

Article

Rational selection of training and test sets for the development of validated QSAR models.

Published in:

Journal of Computer-Aided Molecular Design, 2003, v. 17, n. 2-4, p. 241, doi. 10.1023/A:1025386326946

By:

Golbraikh, Alexander;
Mm Shen;
Zhiyan Xiao;
Yun-de Xiao;
Kuo-Hsiung Lee;
Tropsha, Alexander

Publication type:

Article

Energetic decomposition of the α-helix-coil equilibrium of a dynamic model system.

Published in:

Biopolymers, 1996, v. 39, n. 4, p. 479, doi. 10.1002/(SICI)1097-0282(199610)39:4<479::AID-BIP1>3.0.CO;2-U

By:

Wang, Lu;
O'Connell, Thomas;
Tropsha, Alexander;
Hermans, Jan

Publication type:

Article

Computer-aided design of carbon nanotubes with the desired bioactivity and safety profiles.

Published in:

Nanotoxicology, 2016, v. 10, n. 3, p. 374, doi. 10.3109/17435390.2015.1073397

By:

Fourches, Denis;
Pu, Dongqiuye;
Li, Liwen;
Zhou, Hongyu;
Mu, Qingxin;
Su, Gaoxing;
Yan, Bing;
Tropsha, Alexander

Publication type:

Article

A Systems Biology Workflow for Drug and Vaccine Repurposing: Identifying Small-Molecule BCG Mimics to Reduce or Prevent COVID-19 Mortality.

Published in:

Pharmaceutical Research, 2020, v. 37, n. 11, p. 1, doi. 10.1007/s11095-020-02930-9

By:

Hajjo, Rima;
Tropsha, Alexander

Publication type:

Article

Repurposing Quaternary Ammonium Compounds as Potential Treatments for COVID-19.

Published in:

Pharmaceutical Research, 2020, v. 37, n. 6, p. 1, doi. 10.1007/s11095-020-02842-8

By:

Baker, Nancy;
Williams, Antony J.;
Tropsha, Alexander;
Ekins, Sean

Publication type:

Article

The Use of Pseudo-Equilibrium Constant Affords Improved QSAR Models of Human Plasma Protein Binding.

Published in:

Pharmaceutical Research, 2013, v. 30, n. 7, p. 1790, doi. 10.1007/s11095-013-1023-6

By:

Zhu, Xiang-Wei;
Sedykh, Alexander;
Zhu, Hao;
Liu, Shu-Shen;
Tropsha, Alexander

Publication type:

Article

Human Intestinal Transporter Database: QSAR Modeling and Virtual Profiling of Drug Uptake, Efflux and Interactions.

Published in:

Pharmaceutical Research, 2013, v. 30, n. 4, p. 996, doi. 10.1007/s11095-012-0935-x

By:

Sedykh, Alexander;
Fourches, Denis;
Duan, Jianmin;
Hucke, Oliver;
Garneau, Michel;
Zhu, Hao;
Bonneau, Pierre;
Tropsha, Alexander

Publication type:

Article

A Turning Point For Blood–Brain Barrier Modeling.

Published in:

Pharmaceutical Research, 2009, v. 26, n. 5, p. 1283

By:

Alexander Tropsha

Publication type:

Article

QSAR Modeling of the Blood–Brain Barrier Permeability for Diverse Organic Compounds.

Published in:

Pharmaceutical Research, 2008, v. 25, n. 8, p. 1902, doi. 10.1007/s11095-008-9609-0

By:

Liying Zhang;
Hao Zhu;
Tudor Oprea;
Alexander Golbraikh;
Alexander Tropsha

Publication type:

Article

Structure-based function inference using protein family-specific fingerprints.

Published in:

Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 6, p. 1537, doi. 10.1110/ps.062189906

By:

Bandyopadhyay, Deepak;
Huan, Jun;
Liu, Jinze;
Prins, Jan;
Snoeyink, Jack;
Wang, Wei;
Tropsha, Alexander

Publication type:

Article

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

Published in:

Bioinformatics, 2019, v. 35, n. 24, p. 5382, doi. 10.1093/bioinformatics/btz604

By:

Morton, Kenneth;
Wang, Patrick;
Bizon, Chris;
Cox, Steven;
Balhoff, James;
Kebede, Yaphet;
Fecho, Karamarie;
Tropsha, Alexander

Publication type:

Article

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

Published in:

Bioinformatics, 2019, v. 35, n. 19, p. 3584, doi. 10.1093/bioinformatics/btz127

By:

Farag, Sherif;
Bleich, Rachel M;
Shank, Elizabeth A;
Isayev, Olexandr;
Bowers, Albert A;
Tropsha, Alexander

Publication type:

Article

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

Published in:

Bioinformatics, 2014, v. 30, n. 4, p. 588, doi. 10.1093/bioinformatics/btt718

By:

Fourches, Denis;
Sassano, Maria F.;
Roth, Bryan L.;
Tropsha, Alexander

Publication type:

Article

Chembench: a cheminformatics workbench.

Published in:

Bioinformatics, 2010, v. 26, n. 23, p. 3000, doi. 10.1093/bioinformatics/btq556

By:

Walker, Theo;
Grulke, Christopher M.;
Pozefsky, Diane;
Tropsha, Alexander

Publication type:

Article

Generative and reinforcement learning approaches for the automated de novo design of bioactive compounds.

Published in:

Communications Chemistry, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42004-022-00733-0

By:

Korshunova, Maria;
Huang, Niles;
Capuzzi, Stephen;
Radchenko, Dmytro S.;
Savych, Olena;
Moroz, Yuriy S.;
Wells, Carrow I.;
Willson, Timothy M.;
Tropsha, Alexander;
Isayev, Olexandr

Publication type:

Article

A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service.

Published in:

2019

By:

Fecho, Karamarie;
Pfaff, Emily;
Xu, Hao;
Champion, James;
Cox, Steve;
Stillwell, Lisa;
Peden, David B;
Bizon, Chris;
Krishnamurthy, Ashok;
Tropsha, Alexander;
Ahalt, Stanley C

Publication type:

journal article

Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1822, doi. 10.1002/prot.26587

By:

Kotelnikov, Sergei;
Ashizawa, Ryota;
Popov, Konstantin I.;
Khan, Omeir;
Ignatov, Mikhail;
Stan Xiaogang Li;
Hassan, Mosavverul;
Coutsias, Evangelos A.;
Poda, Gennady;
Padhorny, Dzmitry;
Tropsha, Alexander;
Vajda, Sandor;
Kozakov, Dima

Publication type:

Article

Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.

Published in:

Proteins, 2012, v. 80, n. 9, p. 2207, doi. 10.1002/prot.24110

By:

Khashan, Raed;
Zheng, Weifan;
Tropsha, Alexander

Publication type:

Article

Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening?

Published in:

Proteins, 2012, v. 80, n. 6, p. 1503, doi. 10.1002/prot.24035

By:

Tang, Hao;
Wang, Xiang Simon;
Hsieh, Jui-Hua;
Tropsha, Alexander

Publication type:

Article