Tudor I. Oprea

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 32

Top Topics

Measuring Similarity

Molecular Structures

Top Venues

Nucleic Acids Res.

J. Cheminformatics

J. Comput. Aided Mol. Des.

Database J. Biol. Databases Curation

Publications

Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea
Correction: Exploring DrugCentral: from molecular structures to clinical effects. J. Comput. Aided Mol. Des. 38 (1) (2024)
Sorin I. Avram, Thomas B. Wilson, Ramona Curpan, Liliana Halip, Ana Borota, Alina Bora, Cristian Bologa, Jayme Holmes, Jeffrey Knockel, Jeremy J. Yang, Tudor I. Oprea
DrugCentral 2023 extends human clinical data and integrates veterinary drugs. Nucleic Acids Res. 51 (D1) (2023)
Keith J. Kelleher, Timothy Sheils, Stephen L. Mathias, Jeremy J. Yang, Vincent T. Metzger, Vishal B. Siramshetty, Dac-Trung Nguyen, Lars Juhl Jensen, Dusica Vidovic, Stephan C. Schürer, Jayme Holmes, Karlie R. Sharma, Ajay Pillai, Cristian Bologa, Jeremy S. Edwards, Ewy A. Mathé, Tudor I. Oprea
Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Res. 51 (D1) (2023)
Catrin Hasselgren, Tudor I. Oprea
Artificial Intelligence for Drug Discovery: Are We There Yet? CoRR (2023)
Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea
Exploring DrugCentral: from molecular structures to clinical effects. J. Comput. Aided Mol. Des. 37 (12) (2023)
Gergely Zahoránszky-Köhalmi, Vishal B. Siramshetty, Praveen Kumar, Manideep Gurumurthy, Busola Grillo, Biju Mathew, Dimitrios Metaxatos, Mark Backus, Tim Mierzwa, Reid Simon, Ivan Grishagin, Laura Brovold, Ewy A. Mathé, Matthew D. Hall, Samuel G. Michael, Alexander G. Godfrey, Jordi Mestres, Lars Juhl Jensen, Tudor I. Oprea
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. J. Chem. Inf. Model. 62 (3) (2022)
Dhouha Grissa, Alexander Junge, Tudor I. Oprea, Lars Juhl Jensen
Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration. Database J. Biol. Databases Curation 2022 (2022) (2022)
Jürgen Bajorath, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Eli Fernández-de Gortari, Johann Gasteiger, Edgar López-López, Gerald M. Maggiora, José L. Medina-Franco, Oscar Méndez-Lucio, Jordi Mestres, Ramón Alain Miranda-Quintana, Tudor I. Oprea, Fabien Plisson, Fernando D. Prieto-Martínez, Raquel Rodríguez-Pérez, Paola Rondón-Villarreal, Fernanda I. Saldívar-González, Norberto Sánchez-Cruz, Marilia Valli
Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. J. Cheminformatics 14 (1) (2022)
Timothy Sheils, Stephen L. Mathias, Keith J. Kelleher, Vishal B. Siramshetty, Dac-Trung Nguyen, Cristian Bologa, Lars Juhl Jensen, Dusica Vidovic, Amar Koleti, Stephan C. Schürer, Anna Waller, Jeremy J. Yang, Jayme Holmes, Giovanni Bocci, Noel Southall, Poorva Dharkar, Ewy A. Mathé, Anton Simeonov, Tudor I. Oprea
TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Res. 49 (Database-Issue) (2021)
Kody Moodley, Linda Rieswijk, Tudor I. Oprea, Michel Dumontier
InContext: curation of medical context for drug indications. J. Biomed. Semant. 12 (1) (2021)
Jeremy J. Yang, Dhouha Grissa, Christophe G. Lambert, Cristian Bologa, Stephen L. Mathias, Anna Waller, David J. Wild, Lars Juhl Jensen, Tudor I. Oprea
TIGA: target illumination GWAS analytics. Bioinform. 37 (21) (2021)
Govinda B. Kc, Giovanni Bocci, Srijan Verma, Md Mahmudulla Hassan, Jayme Holmes, Jeremy J. Yang, Suman Sirimulla, Tudor I. Oprea
A machine learning platform to estimate anti-SARS-CoV-2 activities. Nat. Mach. Intell. 3 (6) (2021)
Vladimir Naumov, Evgeny Putin, Stefan Pushkov, Ekaterina Kozlova, Konstantin Romantsov, Alexander A. Kalashnikov, Fedor Galkin, Nina Tihonova, Anastasia Shneyderman, Egor Galkin, Arsenii Zinkevich, Stephanie M. Cope, Ramanathan Sethuraman, Tudor I. Oprea, Alexander T. Pearson, Savas Tay, Nishant Agrawal, Alexey Dubovenko, Quentin Vanhaelen, Ivan Ozerov, Alex Aliper, Evgeny Izumchenko, Alex Zhavoronkov
COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity. PLoS Comput. Biol. 17 (7) (2021)
Sorin I. Avram, Cristian Bologa, Jayme Holmes, Giovanni Bocci, Thomas B. Wilson, Dac-Trung Nguyen, Ramona Curpan, Liliana Halip, Alina Bora, Jeremy J. Yang, Jeffrey Knockel, Suman Sirimulla, Oleg Ursu, Tudor I. Oprea
DrugCentral 2021 supports drug discovery and repositioning. Nucleic Acids Res. 49 (Database-Issue) (2021)
Sorin I. Avram, Ramona Curpan, Liliana Halip, Alina Bora, Tudor I. Oprea
Off-Patent Drug Repositioning. J. Chem. Inf. Model. 60 (12) (2020)
Gergely Zahoránszky-Köhalmi, Timothy Sheils, Tudor I. Oprea
SmartGraph: a network pharmacology investigation platform. J. Cheminformatics 12 (1) (2020)
Oleg Ursu, Jayme Holmes, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Vasileios Stathias, Dac-Trung Nguyen, Stephan C. Schürer, Tudor I. Oprea
DrugCentral 2018: an update. Nucleic Acids Res. 47 (Database-Issue) (2019)
Rodrigo Vazquez Guillamet, Oleg Ursu, Gary Iwamoto, Pope L. Moseley, Tudor I. Oprea
Chronic obstructive pulmonary disease phenotypes using cluster analysis of electronic medical records. Health Informatics J. 24 (4) (2018)
Johann Gasteiger, Yvonne C. Martin, Anthony Nicholls, Tudor I. Oprea, Terry R. Stouch
Leaving us with fond memories, smiles, SMILES and, alas, tears: a tribute to David Weininger, 1952-2016. J. Comput. Aided Mol. Des. 32 (2) (2018)
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J. Yang, Cristian Bologa, Tudor I. Oprea, Stephan C. Schürer
Drug target ontology to classify and integrate drug discovery data. J. Biomed. Semant. 8 (1) (2017)
Qiong Cheng, Felix A. Lopez, Celia Duran, Christopher Camarillo, Tudor I. Oprea, Stephan C. Schürer
The ontology reference model for visual selectivity analysis in drug-target interactions. BIBM (2017)
Daniel Cannon, Jeremy J. Yang, Stephen L. Mathias, Oleg Ursu, Subramani Mani, Anna Waller, Stephan C. Schürer, Lars Juhl Jensen, Larry A. Sklar, Cristian Bologa, Tudor I. Oprea
TIN-X: target importance and novelty explorer. Bioinform. 33 (16) (2017)
Oleg Ursu, Jayme Holmes, Jeffrey Knockel, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Stuart J. Nelson, Tudor I. Oprea
DrugCentral: online drug compendium. Nucleic Acids Res. 45 (Database-Issue) (2017)
Subramani Mani, Daniel Cannon, Robin Ohls, Tudor I. Oprea, Stephen L. Mathias, Karri Ballard, Oleg Ursu, Cristian Bologa
Protein biomarker druggability profiling. J. Biomed. Informatics 66 (2017)
Qiong Cheng, Oleg Ursu, Tudor I. Oprea, Stephan C. Schürer
Learning reference-enriched approach towards large scale active ontology alignment and integration. BIBM (2017)
Dac-Trung Nguyen, Stephen L. Mathias, Cristian Bologa, Søren Brunak, Nicolas F. Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha
Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 45 (Database-Issue) (2017)
Miki Akamatsu, Tudor I. Oprea
Obituary: Toshio Fujita, QSAR pioneer. J. Comput. Aided Mol. Des. 31 (11) (2017)
Stuart J. Nelson, Tudor I. Oprea, Oleg Ursu, Cristian Bologa, Amrapali Zaveri, Jayme Holmes, Jeremy J. Yang, Stephen L. Mathias, Subramani Mani, Mark S. Tuttle, Michel Dumontier
Formalizing drug indications on the road to therapeutic intent. J. Am. Medical Informatics Assoc. 24 (6) (2017)
Jeremy J. Yang, Oleg Ursu, Christopher A. Lipinski, Larry A. Sklar, Tudor I. Oprea, Cristian Bologa
Badapple: promiscuity patterns from noisy evidence. J. Cheminformatics 8 (1) (2016)
Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea
Erratum to: Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. J. Cheminformatics 8 (1) (2016)
Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
ChemProt-3.0: a global chemical biology diseases mapping. Database J. Biol. Databases Curation 2016 (2016)
Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea
Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. J. Cheminformatics 8 (1) (2016)
Subramani Mani, Daniel Cannon, Tudor I. Oprea, Stephen L. Mathias, Oleg Ursu, Cristian Bologa
Protein Drug Target Prioritization for Illumination. AMIA (2015)
Subramani Mani, Joshua Swamidass, Noel Southall, Tudor I. Oprea
Genomic dark matter, druggability and misunderstood targets. AMIA (2014)
Irene Kouskoumvekaki, Rasmus K. Petersen, Filip Fratev, Olivier Taboureau, Thomas E. Nielsen, Tudor I. Oprea, Si B. Sonne, Esben N. Flindt, Svava Ósk Jónsdóttir, Karsten Kristiansen
Work Flow. J. Chem. Inf. Model. 53 (4) (2013)
Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau
ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Res. 41 (Database-Issue) (2013)
Stephen L. Mathias, Jarrett Hines-Kay, Jeremy J. Yang, Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea
The CARLSBAD Database: A Confederated Database of Chemical Bioactivities. Database J. Biol. Databases Curation 2013 (2013)
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 (2013)
Tudor I. Oprea, Olivier Taboureau, Cristian Bologa
Of possible cheminformatics futures. J. Comput. Aided Mol. Des. 26 (1) (2012)
Olivier Taboureau, Sonny Kim Nielsen, Karine Audouze, Nils Weinhold, Daniel Edsgärd, Francisco S. Roque, Irene Kouskoumvekaki, Alina Bora, Ramona Curpan, Thomas Skøt Jensen, Søren Brunak, Tudor I. Oprea
ChemProt: a disease chemical biology database. Nucleic Acids Res. 39 (Database-Issue) (2011)
Ricard García-Serna, Oleg Ursu, Tudor I. Oprea, Jordi Mestres
iPHACE: integrative navigation in pharmacological space. Bioinform. 26 (7) (2010)
Oleg Ursu, Tudor I. Oprea
Model-Free Drug-Likeness from Fragments. J. Chem. Inf. Model. 50 (8) (2010)
Andrew C. Good, Tudor I. Oprea
Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J. Comput. Aided Mol. Des. 22 (3-4) (2008)
Sara N. Pollock, Evangelos A. Coutsias, Michael J. Wester, Tudor I. Oprea
Scaffold Topologies. 1. Exhaustive Enumeration up to Eight Rings. J. Chem. Inf. Model. 48 (7) (2008)
W. Michael Brown, Ariella Sasson, Donald R. Bellew, Lucy A. Hunsaker, Shawn Martin, Andrei Leitão, Lorraine M. Deck, David L. Vander Jagt, Tudor I. Oprea
Efficient Calculation of Molecular Properties from Simulation Using Kernel Molecular Dynamics. J. Chem. Inf. Model. 48 (8) (2008)
Jérôme Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet
Quantifying the Relationships among Drug Classes. J. Chem. Inf. Model. 48 (4) (2008)
Michael J. Wester, Sara N. Pollock, Evangelos A. Coutsias, Tharun Kumar Allu, Sorel Muresan, Tudor I. Oprea
Scaffold Topologies. 2. Analysis of Chemical Databases. J. Chem. Inf. Model. 48 (7) (2008)
Dimitar Hristozov, Tudor I. Oprea, Johann Gasteiger
Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios. J. Comput. Aided Mol. Des. 21 (10-11) (2007)
Tudor I. Oprea, Tharun Kumar Allu, Dan C. Fara, Ramona F. Rad, Lili Ostopovici, Cristian Bologa
Lead-like, drug-like or "Pub-like": how different are they? J. Comput. Aided Mol. Des. 21 (1-3) (2007)
Dimitar Hristozov, Tudor I. Oprea, Johann Gasteiger
Ligand-Based Virtual Screening by Novelty Detection with Self-Organizing Maps. J. Chem. Inf. Model. 47 (6) (2007)
Cristian Bologa, Tharun Kumar Allu, Marius Olah, Michael A. Kappler, Tudor I. Oprea
Descriptor collision and confusion: Toward the design of descriptors to mask chemical structures. J. Comput. Aided Mol. Des. 19 (9-10) (2005)
Igor V. Tetko, Ruben Abagyan, Tudor I. Oprea
Surrogate data - a secure way to share corporate data. J. Comput. Aided Mol. Des. 19 (9-10) (2005)
Tharun Kumar Allu, Tudor I. Oprea
Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry. J. Chem. Inf. Model. 45 (5) (2005)
Ludovic Kurunczi, Edward Seclaman, Tudor I. Oprea, Luminita Crisan, Zeno Simon
MTD-PLS: A PLS Variant of the Minimal Topologic Difference Method. III. Mapping Interactions between Estradiol Derivatives and the Alpha Estrogenic Receptor. J. Chem. Inf. Model. 45 (5) (2005)
Marius Olah, Cristian Bologa, Tudor I. Oprea
An automated PLS search for biologically relevant QSAR descriptors. J. Comput. Aided Mol. Des. 18 (7) (2004)
Tudor I. Oprea
Current trends in lead discovery: Are we looking for the appropriate properties? J. Comput. Aided Mol. Des. 16 (5-6) (2002)
Manuel Pastor, Paolo Benedetti, Angelo Carotti, Antonio Carrieri, Carlos Díaz, Cristina Herráiz, Hans-Dieter Höltje, Maria Isabel Loza, Tudor I. Oprea, Fernando Padín, Francesc Pubill, Ferran Sanz, Friederike Stoll
Distant collaboration in drug discovery: The LINK3D project. J. Comput. Aided Mol. Des. 16 (11) (2002)
Ludovic Kurunczi, Marius Olah, Tudor I. Oprea, Cristian Bologa, Zeno Simon
MTD-PLS: A PLS-Based Variant of the MTD Method, 2. Mapping Ligand-Receptor Interactions. Enzymatic Acetic Acid Esters Hydrolysis. J. Chem. Inf. Comput. Sci. 42 (4) (2002)
Tudor I. Oprea, Andrew M. Davis, Simon J. Teague, Paul D. Leeson
Is There a Difference between Leads and Drugs? A Historical Perspective. J. Chem. Inf. Comput. Sci. 41 (5) (2001)
Tudor I. Oprea
Property distribution of drug-related chemical databases. J. Comput. Aided Mol. Des. 14 (3) (2000)
Traian Sulea, Ludovic Kurunczi, Tudor I. Oprea, Zeno Simon
MTD-ADJ: A multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities. J. Comput. Aided Mol. Des. 12 (2) (1998)
Traian Sulea, Tudor I. Oprea, Sorel Muresan, Shek Ling Chan
A Different Method for Steric Field Evaluation in CoMFA Improves Model Robustness. J. Chem. Inf. Comput. Sci. 37 (6) (1997)
Tudor I. Oprea, Angel E. García
Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors. J. Comput. Aided Mol. Des. 10 (3) (1996)