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2020 – today
- 2024
[j58]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): 2 (2024)- 2023
- [j57]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): 681-694 (2023) - [j56]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): 1276-1287 (2023) - [j55]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): 1405-1416 (2023) - [i1]Catrin Hasselgren, Tudor I. Oprea:
Artificial Intelligence for Drug Discovery: Are We There Yet? CoRR abs/2307.06521 (2023) - 2022
- [j54]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) - [j53]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): 82 (2022) - [j52]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): 718-729 (2022) - 2021
- [j51]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): 3865-3873 (2021) - [j50]Kody Moodley, Linda Rieswijk, Tudor I. Oprea, Michel Dumontier:
InContext: curation of medical context for drug indications. J. Biomed. Semant. 12(1): 2 (2021) - [j49]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): D1160-D1169 (2021) - [j48]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): D1334-D1346 (2021) - [j47]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): 527-535 (2021) - [j46]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) - 2020
- [j45]Gergely Zahoránszky-Köhalmi, Timothy Sheils, Tudor I. Oprea:
SmartGraph: a network pharmacology investigation platform. J. Cheminformatics 12(1): 5 (2020) - [j44]Sorin I. Avram, Ramona Curpan, Liliana Halip, Alina Bora, Tudor I. Oprea:
Off-Patent Drug Repositioning. J. Chem. Inf. Model. 60(12): 5746-5753 (2020)
2010 – 2019
- 2019
- [j43]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): D963-D970 (2019) - 2018
- [j42]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): 394-409 (2018) - [j41]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): 313-319 (2018) - 2017
- [j40]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): 2601-2603 (2017) - [j39]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): 50:1-50:16 (2017) - [j38]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): 1169-1172 (2017) - [j37]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: 241-247 (2017) - [j36]Miki Akamatsu, Tudor I. Oprea:
Obituary: Toshio Fujita, QSAR pioneer. J. Comput. Aided Mol. Des. 31(11): 959-960 (2017) - [j35]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): D932-D939 (2017) - [j34]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): D995-D1002 (2017) - [c4]Qiong Cheng, Oleg Ursu, Tudor I. Oprea, Stephan C. Schürer:
Learning reference-enriched approach towards large scale active ontology alignment and integration. BIBM 2017: 1658-1663 - [c3]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: 2091-2097 - 2016
- [j33]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) - [j32]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): 16:1-16:17 (2016) - [j31]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): 28:1 (2016) - [j30]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): 29:1-29:14 (2016) - 2015
- [c2]Subramani Mani, Daniel Cannon, Tudor I. Oprea, Stephen L. Mathias, Oleg Ursu, Cristian Bologa:
Protein Drug Target Prioritization for Illumination. AMIA 2015 - 2014
- [c1]Subramani Mani, Joshua Swamidass, Noel Southall, Tudor I. Oprea:
Genomic dark matter, druggability and misunderstood targets. AMIA 2014 - 2013
- [j29]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) - [j28]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) - [j27]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:
Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow. J. Chem. Inf. Model. 53(4): 923-937 (2013) - [j26]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): 464-469 (2013) - 2012
- [j25]Tudor I. Oprea, Olivier Taboureau, Cristian Bologa:
Of possible cheminformatics futures. J. Comput. Aided Mol. Des. 26(1): 107-112 (2012) - 2011
- [j24]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): 367-372 (2011) - 2010
- [j23]Ricard García-Serna, Oleg Ursu, Tudor I. Oprea, Jordi Mestres:
iPHACE: integrative navigation in pharmacological space. Bioinform. 26(7): 985-986 (2010) - [j22]Oleg Ursu, Tudor I. Oprea:
Model-Free Drug-Likeness from Fragments. J. Chem. Inf. Model. 50(8): 1387-1394 (2010)
2000 – 2009
- 2008
- [j21]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): 169-178 (2008) - [j20]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): 755-765 (2008) - [j19]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): 1304-1310 (2008) - [j18]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): 1311-1324 (2008) - [j17]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): 1626-1637 (2008) - 2007
- [j16]Tudor I. Oprea, Tharun Kumar Allu, Dan C. Fara, Ramona F. Rad, Liliana Ostopovici, Cristian Bologa:
Lead-like, drug-like or "Pub-like": how different are they? J. Comput. Aided Mol. Des. 21(1-3): 113-119 (2007) - [j15]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): 617-640 (2007) - [j14]Dimitar Hristozov, Tudor I. Oprea, Johann Gasteiger:
Ligand-Based Virtual Screening by Novelty Detection with Self-Organizing Maps. J. Chem. Inf. Model. 47(6): 2044-2062 (2007) - 2005
- [j13]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): 625-635 (2005) - [j12]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): 749-764 (2005) - [j11]Tharun Kumar Allu, Tudor I. Oprea:
Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry. J. Chem. Inf. Model. 45(5): 1237-1243 (2005) - [j10]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): 1275-1281 (2005) - 2004
- [j9]Marius Olah, Cristian Bologa, Tudor I. Oprea:
An automated PLS search for biologically relevant QSAR descriptors. J. Comput. Aided Mol. Des. 18(7): 437-449 (2004) - 2002
- [j8]Tudor I. Oprea:
Current trends in lead discovery: Are we looking for the appropriate properties? J. Comput. Aided Mol. Des. 16(5-6): 325-334 (2002) - [j7]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): 809-818 (2002) - [j6]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): 841-846 (2002) - 2001
- [j5]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): 1308-1315 (2001) - 2000
- [j4]Tudor I. Oprea:
Property distribution of drug-related chemical databases. J. Comput. Aided Mol. Des. 14(3): 251-264 (2000)
1990 – 1999
- 1998
- [j3]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): 133-146 (1998) - 1997
- [j2]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): 1162-1170 (1997) - 1996
- [j1]Tudor I. Oprea, Angel E. García:
Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors. J. Comput. Aided Mol. Des. 10(3): 186-200 (1996)
Coauthor Index
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