Tudor I. Oprea

65 papers Misc 2Journal 61Unranked 2

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
2024	J	`jnl`	Correction: Exploring DrugCentral: from molecular structures to clinical effects. J. Comput. Aided Mol. Des. Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea
2024	J	`jnl`	SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting. J. Chem. Inf. Model. Gergely Zahoránszky-Köhalmi, Brandon Walker, Nathan Miller, Brett Yang, Dhatri V. L. Penna, Jessica Maine, Timothy Sheils, Ke Wang, Jennifer King, Hythem Sidky, Sridhar Vuyyuru, Jeyaraman Soundarajan, Samuel G. Michael, Alexander G. Godfrey, Tudor I. Oprea
2023	J	`jnl`	Artificial Intelligence for Drug Discovery: Are We There Yet? CoRR Catrin Hasselgren, Tudor I. Oprea
2023	J	`jnl`	DrugCentral 2023 extends human clinical data and integrates veterinary drugs. Nucleic Acids Res. 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
2023	J	`jnl`	Exploring DrugCentral: from molecular structures to clinical effects. J. Comput. Aided Mol. Des. Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea
2023	J	`jnl`	Pharos 2023: an integrated resource for the understudied human proteome. Nucleic Acids Res. 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
2022	J	`jnl`	A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. J. Chem. Inf. Model. 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
2022	J	`jnl`	Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. J. Cheminformatics 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
2022	J	`jnl`	Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration. Database J. Biol. Databases Curation Dhouha Grissa, Alexander Junge, Tudor I. Oprea, Lars Juhl Jensen
2021	J	`jnl`	A machine learning platform to estimate anti-SARS-CoV-2 activities. Nat. Mach. Intell. Govinda B. Kc, Giovanni Bocci, Srijan Verma, Md Mahmudulla Hassan, Jayme Holmes, Jeremy J. Yang, Suman Sirimulla, Tudor I. Oprea
2021	J	`jnl`	COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity. PLoS Comput. Biol. 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
2021	J	`jnl`	DrugCentral 2021 supports drug discovery and repositioning. Nucleic Acids Res. 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
2021	J	`jnl`	InContext: curation of medical context for drug indications. J. Biomed. Semant. Kody Moodley, Linda Rieswijk, Tudor I. Oprea, Michel Dumontier
2021	J	`jnl`	TCRD and Pharos 2021: mining the human proteome for disease biology. Nucleic Acids Res. 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
2021	J	`jnl`	TIGA: target illumination GWAS analytics. Bioinform. Jeremy J. Yang, Dhouha Grissa, Christophe G. Lambert, Cristian Bologa, Stephen L. Mathias, Anna Waller, David J. Wild, Lars Juhl Jensen, Tudor I. Oprea
2020	J	`jnl`	Off-Patent Drug Repositioning. J. Chem. Inf. Model. Sorin I. Avram, Ramona Curpan, Liliana Halip, Alina Bora, Tudor I. Oprea
2020	J	`jnl`	SmartGraph: a network pharmacology investigation platform. J. Cheminformatics Gergely Zahoránszky-Köhalmi, Timothy Sheils, Tudor I. Oprea
2019	J	`jnl`	DrugCentral 2018: an update. Nucleic Acids Res. Oleg Ursu, Jayme Holmes, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Vasileios Stathias, Dac-Trung Nguyen, Stephan C. Schürer, Tudor I. Oprea
2018	J	`jnl`	Chronic obstructive pulmonary disease phenotypes using cluster analysis of electronic medical records. Health Informatics J. Rodrigo Vazquez Guillamet, Oleg Ursu, Gary Iwamoto, Pope L. Moseley, Tudor I. Oprea
2018	J	`jnl`	Leaving us with fond memories, smiles, SMILES and, alas, tears: a tribute to David Weininger, 1952-2016. J. Comput. Aided Mol. Des. Johann Gasteiger, Yvonne C. Martin, Anthony Nicholls, Tudor I. Oprea, Terry R. Stouch
2017	J	`jnl`	Drug target ontology to classify and integrate drug discovery data. J. Biomed. Semant. 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
2017	J	`jnl`	DrugCentral: online drug compendium. Nucleic Acids Res. Oleg Ursu, Jayme Holmes, Jeffrey Knockel, Cristian Bologa, Jeremy J. Yang, Stephen L. Mathias, Stuart J. Nelson, Tudor I. Oprea
2017	J	`jnl`	Formalizing drug indications on the road to therapeutic intent. J. Am. Medical Informatics Assoc. 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
2017	—	`conf`	Learning reference-enriched approach towards large scale active ontology alignment and integration. BIBM Qiong Cheng, Oleg Ursu, Tudor I. Oprea, Stephan C. Schürer
2017	J	`jnl`	Obituary: Toshio Fujita, QSAR pioneer. J. Comput. Aided Mol. Des. Miki Akamatsu, Tudor I. Oprea
2017	J	`jnl`	Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 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
2017	J	`jnl`	Protein biomarker druggability profiling. J. Biomed. Informatics Subramani Mani, Daniel Cannon, Robin Ohls, Tudor I. Oprea, Stephen L. Mathias, Karri Ballard, Oleg Ursu, Cristian Bologa
2017	J	`jnl`	TIN-X: target importance and novelty explorer. Bioinform. 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
2017	—	`conf`	The ontology reference model for visual selectivity analysis in drug-target interactions. BIBM Qiong Cheng, Felix A. Lopez, Celia Duran, Christopher Camarillo, Tudor I. Oprea, Stephan C. Schürer
2016	J	`jnl`	Badapple: promiscuity patterns from noisy evidence. J. Cheminformatics Jeremy J. Yang, Oleg Ursu, Christopher A. Lipinski, Larry A. Sklar, Tudor I. Oprea, Cristian Bologa
2016	J	`jnl`	ChemProt-3.0: a global chemical biology diseases mapping. Database J. Biol. Databases Curation Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
2016	J	`jnl`	Erratum to: Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. J. Cheminformatics Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea
2016	J	`jnl`	Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. J. Cheminformatics Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea
2015	Misc	`conf`	Protein Drug Target Prioritization for Illumination. AMIA Subramani Mani, Daniel Cannon, Tudor I. Oprea, Stephen L. Mathias, Oleg Ursu, Cristian Bologa
2014	Misc	`conf`	Genomic dark matter, druggability and misunderstood targets. AMIA Subramani Mani, Joshua Swamidass, Noel Southall, Tudor I. Oprea
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`	ChemProt-2.0: visual navigation in a disease chemical biology database. Nucleic Acids Res. Sonny Kim Kjærulff, Louis Wich, Jens Kringelum, Ulrik Plesner Jacobsen, Irene Kouskoumvekaki, Karine Audouze, Ole Lund, Søren Brunak, Tudor I. Oprea, Olivier Taboureau
2013	J	`jnl`	Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated J. Chem. Inf. Model. 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
2013	J	`jnl`	The CARLSBAD Database: A Confederated Database of Chemical Bioactivities. Database J. Biol. Databases Curation Stephen L. Mathias, Jarrett Hines-Kay, Jeremy J. Yang, Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea
2012	J	`jnl`	Of possible cheminformatics futures. J. Comput. Aided Mol. Des. Tudor I. Oprea, Olivier Taboureau, Cristian Bologa
2011	J	`jnl`	ChemProt: a disease chemical biology database. Nucleic Acids Res. 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
2010	J	`jnl`	Model-Free Drug-Likeness from Fragments. J. Chem. Inf. Model. Oleg Ursu, Tudor I. Oprea
2010	J	`jnl`	iPHACE: integrative navigation in pharmacological space. Bioinform. Ricard García-Serna, Oleg Ursu, Tudor I. Oprea, Jordi Mestres
2008	J	`jnl`	Efficient Calculation of Molecular Properties from Simulation Using Kernel Molecular Dynamics. J. Chem. Inf. Model. 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
2008	J	`jnl`	Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J. Comput. Aided Mol. Des. Andrew C. Good, Tudor I. Oprea
2008	J	`jnl`	Quantifying the Relationships among Drug Classes. J. Chem. Inf. Model. Jérôme Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet
2008	J	`jnl`	Scaffold Topologies. 1. Exhaustive Enumeration up to Eight Rings. J. Chem. Inf. Model. Sara N. Pollock, Evangelos A. Coutsias, Michael J. Wester, Tudor I. Oprea
2008	J	`jnl`	Scaffold Topologies. 2. Analysis of Chemical Databases. J. Chem. Inf. Model. Michael J. Wester, Sara N. Pollock, Evangelos A. Coutsias, Tharun Kumar Allu, Sorel Muresan, Tudor I. Oprea
2007	J	`jnl`	Lead-like, drug-like or "Pub-like": how different are they? J. Comput. Aided Mol. Des. Tudor I. Oprea, Tharun Kumar Allu, Dan C. Fara, Ramona F. Rad, Liliana Ostopovici, Cristian Bologa
2007	J	`jnl`	Ligand-Based Virtual Screening by Novelty Detection with Self-Organizing Maps. J. Chem. Inf. Model. Dimitar Hristozov, Tudor I. Oprea, Johann Gasteiger
2007	J	`jnl`	Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios. J. Comput. Aided Mol. Des. Dimitar Hristozov, Tudor I. Oprea, Johann Gasteiger
2005	J	`jnl`	Descriptor collision and confusion: Toward the design of descriptors to mask chemical structures. J. Comput. Aided Mol. Des. Cristian Bologa, Tharun Kumar Allu, Marius Olah, Michael A. Kappler, Tudor I. Oprea
2005	J	`jnl`	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. Ludovic Kurunczi, Edward Seclaman, Tudor I. Oprea, Luminita Crisan, Zeno Simon
2005	J	`jnl`	Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry. J. Chem. Inf. Model. Tharun Kumar Allu, Tudor I. Oprea
2005	J	`jnl`	Surrogate data - a secure way to share corporate data. J. Comput. Aided Mol. Des. Igor V. Tetko, Ruben Abagyan, Tudor I. Oprea
2004	J	`jnl`	An automated PLS search for biologically relevant QSAR descriptors. J. Comput. Aided Mol. Des. Marius Olah, Cristian Bologa, Tudor I. Oprea
2002	J	`jnl`	Current trends in lead discovery: Are we looking for the appropriate properties? J. Comput. Aided Mol. Des. Tudor I. Oprea
2002	J	`jnl`	Distant collaboration in drug discovery: The LINK3D project. J. Comput. Aided Mol. Des. Manuel Pastor, Paolo Benedetti, Angelo Carotti, Antonio Carrieri, Carlos Díaz, Cristina Herráiz, Hans-Dieter Höltje, María Isabel Loza, Tudor I. Oprea, Fernando Padín, Francesc Pubill, Ferran Sanz, Friederike Stoll
2002	J	`jnl`	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. Ludovic Kurunczi, Marius Olah, Tudor I. Oprea, Cristian Bologa, Zeno Simon
2001	J	`jnl`	Is There a Difference between Leads and Drugs? A Historical Perspective. J. Chem. Inf. Comput. Sci. Tudor I. Oprea, Andrew M. Davis, Simon J. Teague, Paul D. Leeson
2000	J	`jnl`	Property distribution of drug-related chemical databases. J. Comput. Aided Mol. Des. Tudor I. Oprea
1998	J	`jnl`	MTD-ADJ: A multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities. J. Comput. Aided Mol. Des. Traian Sulea, Ludovic Kurunczi, Tudor I. Oprea, Zeno Simon
1997	J	`jnl`	A Different Method for Steric Field Evaluation in CoMFA Improves Model Robustness. J. Chem. Inf. Comput. Sci. Traian Sulea, Tudor I. Oprea, Sorel Muresan, Shek Ling Chan
1996	J	`jnl`	Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors. J. Comput. Aided Mol. Des. Tudor I. Oprea, Angel E. García