Shoichet, Brian K.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., et al. (2020) · Nature

SARS-CoV-2 and COVID-19 ResearchComputational Drug Discovery Methods

Cited by 4,405

ZINC − A Free Database of Commercially Available Compounds for Virtual Screening

Irwin, J. J., & Shoichet, B. K. (2005) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsSynthesis and Characterization of Heterocyclic Compounds

Cited by 4,058

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.

Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K. (2012) · Journal of Medicinal Chemistry

Computational Drug Discovery MethodsProtein Degradation and Inhibitors

Cited by 2,412

Relating protein pharmacology by ligand chemistry

Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., & Shoichet, B. K. (2007) · Nature Biotechnology

Computational Drug Discovery MethodsReceptor Mechanisms and Signaling

Cited by 2,402

Predicting new molecular targets for known drugs

Keiser, M. J., Setola, V., Irwin, J. J., Laggner, C., Abbas, A. I., Hufeisen, S. J., Jensen, N. H., Kuijer, M. B., Matos, R. C., Tran, T. B., et al. (2009) · Nature

Computational Drug Discovery MethodsReceptor Mechanisms and Signaling

Cited by 1,667

Virtual screening of chemical libraries

Shoichet, B. K. (2004) · Nature

Computational Drug Discovery MethodsReceptor Mechanisms and Signaling

Cited by 1,425

Benchmarking sets for molecular docking.

Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry

Computational Drug Discovery MethodsProtein Degradation and Inhibitors

Cited by 1,318

Ultra-large library docking for discovering new chemotypes

Lyu, J., Wang, S., Balius, T. E., Singh, I., Levit, A., Moroz, Y. S., O’Meara, M. J., Che, T., Algaa, E., Tolmachova, K., et al. (2019) · Nature

Computational Drug Discovery MethodsSynthesis and Characterization of Heterocyclic Compounds

Cited by 998

The promise and peril of chemical probes

Arrowsmith, C. H., Audia, J. E., Austin, C., Baell, J., Bennett, J., Blagg, J., Bountra, C., Brennan, P. E., Brown, P. J., Bunnage, M. E., et al. (2015) · Nature Chemical Biology

Click Chemistry and ApplicationsComputational Drug Discovery Methods

Cited by 839

A practical guide to large-scale docking

Bender, B. J., Gahbauer, S., Luttens, A., Lyu, J., Webb, C. M., Stein, R. M., Fink, E. A., Balius, T. E., Carlsson, J., Irwin, J. J., et al. (2021) · Nature Protocols

Computational Drug Discovery MethodsReceptor Mechanisms and Signaling

Cited by 546

Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor

Kim, K., Che, T., Panova, O., DiBerto, J. F., Lyu, J., Krumm, B. E., Wacker, D., Robertson, M. J., Seven, A. B., Nichols, D. E., et al. (2020) · Cell

Receptor Mechanisms and SignalingPsychedelics and Drug Studies

Cited by 481

Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

Mobley, D. L., Graves, A. P., Chodera, J. D., McReynolds, A. C., Shoichet, B. K., & Dill, K. A. (2007) · Journal of Molecular Biology

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 310

Interpreting steep dose-response curves in early inhibitor discovery.

Shoichet, B. K. (2006) · Journal of Medicinal Chemistry

Enzyme function and inhibitionComputational Drug Discovery Methods

Cited by 304

In silico design of novel probes for the atypical opioid receptor MRGPRX2

Lansu, K., Karpiak, J., Liu, J., Huang, X.-P., McCorvy, J. D., Kroeze, W. K., Che, T., Nagase, H., Carroll, F. I., Jin, J., et al. (2017) · Nature Chemical Biology

Computational Drug Discovery MethodsReceptor Mechanisms and Signaling

Cited by 293

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

Huang, X.-P., Karpiak, J., Kroeze, W. K., Zhu, H., Chen, X., Moy, S. S., Saddoris, K. A., Nikolova, V. D., Farrell, M. S., Wang, S., et al. (2015) · Nature

Receptor Mechanisms and SignalingComputational Drug Discovery Methods

Cited by 284

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

McGovern, S. L., & Shoichet, B. K. (2003) · Journal of Medicinal Chemistry

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 276

Covalent docking of large libraries for the discovery of chemical probes

London, N., Miller, R. M., Krishnan, S., Uchida, K., Irwin, J. J., Eidam, O., Gibold, L., Cimermančič, P., Bonnet, R., Shoichet, B. K., et al. (2014) · Nature Chemical Biology

Computational Drug Discovery MethodsClick Chemistry and Applications

Cited by 274

A model binding site for testing scoring functions in molecular docking.

Wei, B. Q., Baase, W. A., Weaver, L. H., Matthews, B. W., & Shoichet, B. K. (2002) · Journal of Molecular Biology

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 237

Structures of the σ2 receptor enable docking for bioactive ligand discovery

Alon, A., Lyu, J., Braz, J. M., Tummino, T. A., Craik, V., O’Meara, M. J., Webb, C. M., Radchenko, D. S., Moroz, Y. S., Huang, X.-P., et al. (2021) · Nature

Pharmacological Receptor Mechanisms and EffectsReceptor Mechanisms and Signaling

Cited by 211

Modeling the expansion of virtual screening libraries

Lyu, J., Irwin, J. J., & Shoichet, B. K. (2023) · Nature Chemical Biology

Computational Drug Discovery MethodsChemical Synthesis and Analysis

Cited by 193

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.

Fischer, M., Coleman, R. G., Fraser, J. S., & Shoichet, B. K. (2014) · Nature Chemistry

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 149

Molecular Docking Screens Using Comparative Models of Proteins

Fan, H., Irwin, J. J., Webb, B. M., Klebe, G., Shoichet, B. K., & Sali, A. (2009) · Journal of Chemical Information and Modeling

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 135

Discovery of new GPCR ligands to illuminate new biology

Roth, B. L., Irwin, J. J., & Shoichet, B. K. (2017) · Nature Chemical Biology

Receptor Mechanisms and SignalingComputational Drug Discovery Methods

Cited by 94

Divergent modes of enzyme inhibition in a homologous structure-activity series.

Ferreira, R. S., Bryant, C., Ang, K. K. H., McKerrow, J. H., Shoichet, B. K., & Renslo, A. R. (2009) · Journal of Medicinal Chemistry

Trypanosoma species research and implicationsProtease and Inhibitor Mechanisms

Cited by 88