Oprea, Tudor I.

A comprehensive map of molecular drug targets

Santos, R., Ursu, O., Gaulton, A., Bento, A. P., Donadi, R. S., Bologa, C. G., Karlsson, A., Al-Lazikani, B., Hersey, A., Oprea, T. I., et al. (2017) · Nature Reviews Drug Discovery

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 2,427

QSAR without borders

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., Oprea, T. I., Baskin, I. I., Varnek, A., Roitberg, A., et al. (2020) · Chemical Society Reviews

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 913

How many rare diseases are there?

Haendel, M., Vasilevsky, N., Unni, D., Bologa, C., Harris, N., Rehm, H., Hamosh, A., Baynam, G., Groza, T., McMurry, J., et al. (2020) · Nature Reviews Drug Discovery

Genomics and Rare DiseasesGenetic Associations and Epidemiology

Cited by 554

Unexplored therapeutic opportunities in the human genome

Oprea, T. I., Bologa, C. G., Brunak, S., Campbell, A., Gan, G. N., Gaulton, A., Gomez, S. M., Guha, R., Hersey, A., Holmes, J., et al. (2018) · Nature Reviews Drug Discovery

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 378

Therapies for rare diseases: therapeutic modalities, progress and challenges ahead

Tambuyzer, E., Vandendriessche, B., Austin, C. P., Brooks, P. J., Larsson, K., Miller Needleman, K. I., Valentine, J., Davies, K., Groft, S. C., Preti, R., et al. (2020) · Nature Reviews Drug Discovery

Pharmaceutical Economics and PolicyGenomics and Rare Diseases

Cited by 357

DrugCentral: online drug compendium

Ursu, O., Holmes, J., Knockel, J., Bologa, C. G., Yang, J. J., Mathias, S. L., Nelson, S. J., & Oprea, T. I. (2017) · Nucleic Acids Research

Computational Drug Discovery MethodsBiomedical Text Mining and Ontologies

Cited by 323

Drug repurposing: far beyond new targets for old drugs

Oprea, T. I., & Mestres, J. (2012) · The AAPS Journal

Computational Drug Discovery MethodsPharmaceutical Economics and Policy

Cited by 285

Pharos: collating protein information to shed light on the druggable genome

Nguyen, D.-T., Mathias, S., Bologa, C., Brunak, S., Fernandez, N., Gaulton, A., Hersey, A., Holmes, J., Jensen, L. J., Karlsson, A., et al. (2017) · Nucleic Acids Research

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 279

Understanding drug‐likeness

Ursu, O., Rayan, A., Goldblum, A., & Oprea, T. I. (2011) · WIREs Computational Molecular Science

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 276

In silico toxicology protocols

Myatt, G. J., Ahlberg, E., Akahori, Y., Allen, D., Amberg, A., Anger, L. T., Aptula, A., Auerbach, S., Beilke, L., Bellion, P., et al. (2018) · Regulatory Toxicology and Pharmacology

Computational Drug Discovery MethodsAnimal testing and alternatives

Cited by 240

Artificial Intelligence for Drug Discovery: Are We There Yet?

Hasselgren, C., & Oprea, T. I. (2024) · Annual Review of Pharmacology and Toxicology

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 236

A critical overview of computational approaches employed for COVID-19 drug discovery

Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J. L., Merz, K. M., et al. (2021) · Chemical Society Reviews

Computational Drug Discovery MethodsSARS-CoV-2 and COVID-19 Research

Cited by 206

DrugCentral 2021 supports drug discovery and repositioning

Avram, S., Bologa, C. G., Holmes, J., Bocci, G., Wilson, T. B., Nguyen, D.-T., Curpan, R., Halip, L., Bora, A., Yang, J. J., et al. (2021) · Nucleic Acids Research

Computational Drug Discovery MethodsPharmacovigilance and Adverse Drug Reactions

Cited by 189

TCRD and pharos 2021: mining the human proteome for disease biology

Sheils, T. K., Mathias, S. L., Kelleher, K. J., Siramshetty, V. B., Nguyen, D.-T., Bologa, C. G., Jensen, L. J., Vidović, D., Koleti, A., Schürer, S. C., et al. (2021) · Nucleic Acids Research

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 160

Will Artificial Intelligence for Drug Discovery Impact Clinical Pharmacology?

Zhavoronkov, A., Vanhaelen, Q., & Oprea, T. I. (2020) · Clinical Pharmacology & Therapeutics

Computational Drug Discovery MethodsArtificial Intelligence in Healthcare and Education

Cited by 159

Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration

Grissa, D., Junge, A., Oprea, T. I., & Jensen, L. J. (2022) · Database

Biomedical Text Mining and OntologiesBioinformatics and Genomic Networks

Cited by 144

Pharos 2023: an integrated resource for the understudied human proteome

Kelleher, K. J., Sheils, T. K., Mathias, S. L., Yang, J. J., Metzger, V. T., Siramshetty, V. B., Nguyen, D.-T., Jensen, L. J., Vidović, D., Schürer, S. C., et al. (2023) · Nucleic Acids Research

Computational Drug Discovery MethodsBioinformatics and Genomic Networks

Cited by 137

Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer’s disease

Xu, J., Mao, C., Hou, Y., Luo, Y., Binder, J. L., Zhou, Y., Bekris, L. M., Shin, J., Hu, M., Wang, F., et al. (2022) · Cell Reports

Alzheimer's disease research and treatmentsBioinformatics and Genomic Networks

Cited by 115

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Ackloo, S., Al-awar, R., Amaro, R. E., Arrowsmith, C. H., Azevedo, H., Batey, R. A., Bengio, Y., Betz, U. A. K., Bologa, C. G., Chodera, J. D., et al. (2022) · Nature Reviews Chemistry

Computational Drug Discovery MethodsProtein Degradation and Inhibitors

Cited by 112

Mondo: Unifying diseases for the world, by the world

Vasilevsky, N. A., Matentzoglu, N. A., Toro, S., Flack, J. E., Hegde, H., Unni, D. R., Alyea, G. F., Amberger, J. S., Babb, L., Balhoff, J. P., et al. (2022) · medRxiv

Biomedical Text Mining and OntologiesSemantic Web and Ontologies

Cited by 107

Badapple: promiscuity patterns from noisy evidence

Yang, J. J., Ursu, O., Lipinski, C. A., Sklar, L. A., Oprea, T. I., & Bologa, C. G. (2016) · Journal of Cheminformatics

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 103

DrugCentral 2023 extends human clinical data and integrates veterinary drugs

Avram, S., Wilson, T. B., Curpan, R., Halip, L., Borota, A., Bora, A., Bologa, C. G., Holmes, J., Knockel, J., Yang, J. J., et al. (2023) · Nucleic Acids Research

Computational Drug Discovery MethodsPharmacovigilance and Adverse Drug Reactions

Cited by 101

An automated PLS search for biologically relevant QSAR descriptors

Olah, M., Bologa, C., & Oprea, T. I. (2004) · Journal of Computer-Aided Molecular Design

Computational Drug Discovery MethodsMachine Learning in Materials Science

Cited by 91

AlphaFold illuminates half of the dark human proteins

Binder, J. L., Berendzen, J., Stevens, A. O., He, Y., Wang, J., Dokholyan, N. V., & Oprea, T. I. (2022) · Current Opinion in Structural Biology

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 81