B. Shoichet

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ZINC ? A Free Database of Commercially Available Compounds for Virtual Screening.

J. Irwin, B. Shoichet, 2005 .

Protein docking and complementarity.

I. Kuntz, B. Shoichet, 1991, Journal of molecular biology.

Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.

B. Shoichet, T. Doman, S. McGovern, 2002, Journal of medicinal chemistry.

Predicting new molecular targets for known drugs

Michael J. Keiser, J. Irwin, B. Shoichet, 2009, Nature.

Flexible ligand docking using conformational ensembles

B. Shoichet, D. Lorber, 1998, Protein science : a publication of the Protein Society.

Relating protein pharmacology by ligand chemistry

Michael J. Keiser, J. Irwin, B. Shoichet, 2007, Nature Biotechnology.

Structure-based activity prediction for an enzyme of unknown function

Johannes C. Hermann, B. Shoichet, Ricardo Martí-Arbona, 2007, Nature.

Prediction of Protein—Ligand Interactions. Docking and Scoring: Successes and Gaps

A. Leach, B. Shoichet, C. E. Peishoff, 2006 .

Large Scale Prediction and Testing of Drug Activity on Side-Effect Targets

Michael J. Keiser, B. Shoichet, J. Jenkins, 2012, Nature.

The Chemical Basis of Pharmacology

Michael J. Keiser, J. Irwin, B. Shoichet, 2010, Biochemistry.

Docking and chemoinformatic screens for new ligands and targets.

J. Irwin, B. Shoichet, P. Kolb, 2009, Current opinion in biotechnology.

A specific mechanism of nonspecific inhibition.

B. Shoichet, S. McGovern, B. Helfand, 2003, Journal of medicinal chemistry.

Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.

Michael J. Keiser, B. Shoichet, A. Degraw, 2010, Journal of medicinal chemistry.

High-throughput assays for promiscuous inhibitors

B. Shoichet, T. Doman, Brian Y Feng, 2005, Nature chemical biology.

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

Michael M. Mysinger, J. Irwin, B. Shoichet, 2012, Journal of medicinal chemistry.

Matching chemistry and shape in molecular docking.

I. Kuntz, B. Shoichet, 1993, Protein engineering.

A Survey of Antiprion Compounds Reveals the Prevalence of Non-PrP Molecular Targets*

S. Prusiner, S. Ghaemmaghami, B. Shoichet, 2011, The Journal of Biological Chemistry.

Ultra-large library docking for discovering new chemotypes

Yurii S. Moroz, Matthew J. O’Meara, J. Irwin, 2019, Nature.

ChemInform Abstract: Quantifying the Relationships among Drug Classes.

Tudor I. Oprea, Michael J. Keiser, T. Oprea, 2008 .

Structure-Based Molecular Design

I. Kuntz, B. Shoichet, E. Meng, 1994 .

Rapid Context-Dependent Ligand Desolvation in Molecular Docking

Brian K. Shoichet, Michael M. Mysinger, B. Shoichet, 2010, J. Chem. Inf. Model..

Probing molecular docking in a charged model binding site.

B. Shoichet, R. Brenk, S. Vetter, 2006, Journal of molecular biology.

Automated docking with grid‐based energy evaluation

I. Kuntz, B. Shoichet, E. Meng, 1992 .

Decoys for docking.

B. Shoichet, R. Brenk, A. P. Graves, 2005, Journal of medicinal chemistry.

Lead discovery using molecular docking.

J. Irwin, B. Shoichet, S. McGovern, 2002, Current opinion in chemical biology.

Hierarchical docking of databases of multiple ligand conformations.

B. Shoichet, D. Lorber, 2005, Current topics in medicinal chemistry.

Automated Docking Screens: A Feasibility Study

Michael M. Mysinger, J. Irwin, B. Shoichet, 2009, Journal of medicinal chemistry.

Rescoring docking hit lists for model cavity sites: predictions and experimental testing.

D. Case, B. Shoichet, M. Jacobson, 2008, Journal of molecular biology.

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

B. Matthews, B. Shoichet, W. Baase, 2002, Journal of molecular biology.

Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation

B. Matthews, B. Shoichet, W. Baase, 2001, Proteins.

Benchmarking sets for molecular docking.

J. Irwin, B. Shoichet, N. Huang, 2006, Journal of medicinal chemistry.

No free energy lunch

B. Shoichet, 2007, Nature Biotechnology.

Ligand solvation in molecular docking

I. Kuntz, A. Leach, B. Shoichet, 1999, Proteins.

A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening.

B. Shoichet, S. McGovern, N. Grigorieff, 2002, Journal of medicinal chemistry.

Structure-based discovery of inhibitors of thymidylate synthase.

I. Kuntz, B. Shoichet, R. Stroud, 1993, Science.

Homologous ligands accommodated by discrete conformations of a buried cavity

Brian K. Shoichet, Trent E. Balius, Marcus Fischer, 2015, Proceedings of the National Academy of Sciences.

Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme.

B K Shoichet, B. Shoichet, W. Baase, 1999, Biochemistry.

A relationship between protein stability and protein function.

B K Shoichet, B. Matthews, B. Shoichet, 1995, Proceedings of the National Academy of Sciences of the United States of America.

The Enzyme Function Initiative.

Heidi J. Imker, Karen N. Allen, A. Sali, 2011, Biochemistry.

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.

Brian K Shoichet, Andrew R Leach, A. Leach, 2006, Journal of medicinal chemistry.

Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase

J. Cherfils, R. Abagyan, I. Kuntz, 1996, Nature Structural Biology.

Soft docking and multiple receptor conformations in virtual screening.

B. Shoichet, A. Ferrari, BinQing Wei, 2004, Journal of medicinal chemistry.

A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

Benjamin J. Polacco, Robyn M. Kaake, Gwendolyn M. Jang, 2020, Nature.

Identifying mechanism-of-action targets for drugs and probes

J. Irwin, B. Shoichet, V. Setola, 2012, Proceedings of the National Academy of Sciences.

Molecular docking and ligand specificity in fragment-based inhibitor discovery.

B. Shoichet, Yu Chen, 2009, Nature chemical biology.

Screening in a spirit haunted world.

B. Shoichet, 2006, Drug discovery today.

Docking Screens for Novel Ligands Conferring New Biology.

J. Irwin, B. Shoichet, 2016, Journal of medicinal chemistry.

Structure-based Discovery of Antagonists of Nuclear Receptor LRH-1*

R. Fletterick, J. Irwin, B. Shoichet, 2013, The Journal of Biological Chemistry.

Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.

A. Sali, B. Shoichet, Hao Fan, 2015, Journal of medicinal chemistry.

Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.

Maria Paola Costi, Michael E. Nelson, J. Irwin, 2008, Journal of medicinal chemistry.

An Aggregation Advisor for Ligand Discovery.

J. Irwin, B. Shoichet, Allison K. Doak, 2015, Journal of medicinal chemistry.

Complementarity Between a Docking and a High-Throughput Screen in Discovering New Cruzain Inhibitors†

Michael J. Keiser, J. Irwin, B. Shoichet, 2010, Journal of medicinal chemistry.

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.

B. Shoichet, S. McGovern, 2003, Journal of medicinal chemistry.

Predicting absolute ligand binding free energies to a simple model site.

K. Dill, D. Mobley, B. Shoichet, 2007, Journal of molecular biology.

Blind prediction of charged ligand binding affinities in a model binding site.

K. Dill, D. Mobley, B. Shoichet, 2013, Journal of molecular biology.

Identification and prediction of promiscuous aggregating inhibitors among known drugs.

B. Shoichet, T. Doman, S. McGovern, 2003, Journal of medicinal chemistry.

The Recognition of Identical Ligands by Unrelated Proteins.

Matthew J. O’Meara, B. Shoichet, S. Barelier, 2015, ACS chemical biology.

Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets

W. DuMouchel, B. Shoichet, Eugen Lounkine, 2017, eLife.

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

D. E. Nichols, B. Shoichet, B. Roth, 2020, Cell.

Crystal Structure of an LSD-Bound Human Serotonin Receptor

D. E. Nichols, R. Dror, B. Shoichet, 2017, Cell.

Substrate Deconstruction and the Nonadditivity of Enzyme Recognition

Daniel S. Hitchcock, Karen N. Allen, B. Shoichet, 2014, Journal of the American Chemical Society.

An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation.

B. Shoichet, G. Minasov, Xiaojun Wang, 2002, Journal of the American Chemical Society.

Structural basis for imipenem inhibition of class C beta-lactamases.

B. Shoichet, B. Beadle, 2010, Antimicrobial agents and chemotherapy.

The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution.

B. Shoichet, R. Bonnet, Yu Chen, 2007, Journal of the American Chemical Society.

The Acylation Mechanism of CTX-M β-Lactamase at 0.88 Å Resolution

B. Shoichet, R. Bonnet, Yu Chen, 2007 .

Docking for fragment inhibitors of AmpC β-lactamase

Denise G. Teotico, B. Shoichet, R. S. Ferreira, 2009, Proceedings of the National Academy of Sciences.

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

A. Ashworth, J. Irwin, B. Shoichet, 2020, Science Advances.

Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives

B. Shoichet, P. Turnbaugh, K. Giacomini, 2020, Proceedings of the National Academy of Sciences.

Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.

Brian K Shoichet, B. Shoichet, G. Minasov, 2002, Journal of molecular biology.

Structural bases of stability-function tradeoffs in enzymes.

Beth M Beadle, Brian K Shoichet, B. Shoichet, 2002, Journal of molecular biology.

A detergent-based assay for the detection of promiscuous inhibitors

Brian K Shoichet, B. Shoichet, Brian Y Feng, 2006, Nature Protocols.

A high-throughput screen for aggregation-based inhibition in a large compound library.

Christopher P Austin, Anton Simeonov, James Inglese, 2007, Journal of medicinal chemistry.

Quantifying Biogenic Bias in Screening Libraries

Jérôme Hert, Brian K. Shoichet, Michael J. Keiser, 2009, Nature chemical biology.

Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets

Dahlia R. Weiss, Bryan L Roth, Brian K Shoichet, 2018, Journal of medicinal chemistry.

Testing a flexible-receptor docking algorithm in a model binding site.

Brian K Shoichet, Brian W Matthews, B. Matthews, 2004, Journal of molecular biology.

Protein–protein docking with multiple residue conformations and residue substitutions

Brian K Shoichet, B. Shoichet, D. Lorber, 2002, Protein science : a publication of the Protein Society.

Virtual screening against metalloenzymes for inhibitors and substrates.

John J Irwin, Brian K Shoichet, J. Irwin, 2005, Biochemistry.

Predicting substrates by docking high-energy intermediates to enzyme structures.

John J Irwin, Johannes C. Hermann, Brian K Shoichet, 2006, Journal of the American Chemical Society.

Exploiting ordered waters in molecular docking.

Niu Huang, Brian K Shoichet, B. Shoichet, 2008, Journal of medicinal chemistry.

Deconstructing fragment-based inhibitor discovery

Kerim Babaoglu, Brian K Shoichet, B. Shoichet, 2006, Nature chemical biology.

Structural aspects for evolution of beta-lactamases from penicillin-binding proteins.

Samy O Meroueh, Brian K Shoichet, B. Shoichet, 2003, Journal of the American Chemical Society.

Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis.

N Srinivasan, R Sowdhamini, B Shoichet, 1989, Protein engineering.

The Importance of Reverse Translation for Preclinical Off-Target Mitigation: Quantification and Mitigation of Biases in the FDA Adverse Event Reporting System

B. Shoichet, Eugen Lounkine, S. Whitebread, 2017, bioRxiv.

The Powers and Perils of Post-Marketing Data Analysis: Quantification and Mitigation of Biases in the FDA Adverse Event Reporting System

B. Shoichet, Eugen Lounkine, S. Whitebread, 2016 .

Discovery of new GPCR ligands to illuminate new biology.

Bryan L Roth, John J Irwin, Brian K Shoichet, 2017, Nature chemical biology.

Identification of Novel Smoothened Ligands Using Structure-Based Docking

Hayarpi Torosyan, John J Irwin, Brian K Shoichet, 2016, PloS one.

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

Andrew R. Leach, Anna Gaulton, Aurelien Dugourd, 2020, Cell.

Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET

Avner Schlessinger, Andrej Sali, John J Irwin, 2011, Proceedings of the National Academy of Sciences.

Ligand Discovery from a Dopamine D3 Receptor Homology Model and Crystal Structure

Avner Schlessinger, Bryan L. Roth, Brian K. Shoichet, 2011, Nature chemical biology.

Colloidal Drug Formulations Can Explain “Bell-Shaped” Concentration–Response Curves

Brian K. Shoichet, Shawn C. Owen, B. Shoichet, 2014, ACS chemical biology.

Colloidal Aggregation Causes Inhibition of G Protein-Coupled Receptors

Maria F. Sassano, Bryan L. Roth, Brian K. Shoichet, 2013, Journal of medicinal chemistry.

Chemical Informatics and Target Identification in a Zebrafish Phenotypic Screen

Bryan L. Roth, Brian K. Shoichet, Michael J. Keiser, 2011, Nature chemical biology.

Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability.

Richard Bonnet, Brian Shoichet, B. Shoichet, 2005, Journal of molecular biology.

Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo

B. Shoichet, E. Caselli, O. Eidam, 2012, Proceedings of the National Academy of Sciences.

Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase.

B K Shoichet, B. Shoichet, S. Ghelli, 1999, Chemistry & biology.

Promiscuous Aggregate-Based Inhibitors Promote Enzyme Unfolding

Kristin E. D. Coan, A. Burlingame, B. Shoichet, 2009, Journal of medicinal chemistry.

Protein stability effects in aggregate-based enzyme inhibition.

Brian K. Shoichet, Hayarpi Torosyan, B. Shoichet, 2019, Journal of medicinal chemistry.

Colloidal aggregation: from screening nuisance to formulation nuance.

Brian K Shoichet, B. Shoichet, M. Shoichet, 2018, Nano today.

Structure-based drug screening for G-protein-coupled receptors.

Brian K Shoichet, B. Shoichet, B. Kobilka, 2012, Trends in pharmacological sciences.

Colloid Formation by Drugs in Simulated Intestinal Fluid

S. Prusiner, B. Shoichet, Allison K. Doak, 2010, Journal of medicinal chemistry.

Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase.

G S Weston, B K Shoichet, B. Shoichet, 1998, Journal of medicinal chemistry.

Kinase inhibitors: not just for kinases anymore.

Brian K Shoichet, B. Shoichet, S. McGovern, 2003, Journal of medicinal chemistry.

Interpreting steep dose-response curves in early inhibitor discovery.

Brian K Shoichet, B. Shoichet, 2006, Journal of medicinal chemistry.

Inhibitor Design from Known Structures

I. Kuntz, B. Shoichet, R. DesJarlais, 1990 .

Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive.

B K Shoichet, B. Matthews, B. Shoichet, 1995, Protein engineering.

A Pharmacological Organization of G Protein-coupled Receptors

Maria F. Sassano, Bryan L. Roth, Brian K. Shoichet, 2012, Nature Methods.

The Recognition of Unrelated Ligands by Identical Proteins.

B. Shoichet, A. Levit, M. Fischer, 2018, ACS chemical biology.

Structure-Based Design and Discovery of New M2 Receptor Agonists.

B. Shoichet, A. Christopoulos, R. Sunahara, 2017, Journal of medicinal chemistry.

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

Jing Liu, Jian Jin, John D. McCorvy, 2016, Nature chemical biology.

Structure-Based Design and Discovery of New M2 Receptor Agonists.

B. Shoichet, A. Christopoulos, R. Sunahara, 2017, Journal of medicinal chemistry.

In Vitro and In Vivo Characterization of the Alkaloid Nuciferine

Alison I. Bernstein, B. Shoichet, R. Rodriguiz, 2016, PloS one.

Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4)

Brian K. Shoichet, Ryan G. Coleman, B. Shoichet, 2013, Biochemical pharmacology.

Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor

Maria F. Sassano, Bryan L. Roth, Brian K. Shoichet, 2013, ACS chemical biology.

Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor

Dahlia R. Weiss, B. Shoichet, Joanne Baltos, 2018, Proceedings of the National Academy of Sciences.

Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs

Kyle V. Butler, R. Dror, B. Shoichet, 2017, Nature chemical biology.

Structural identification of a hotspot on CFTR for potentiation.

B. Shoichet, A. Levit, Jue Chen, 2019 .

A Molecular Docking Strategy Identifies Eosin B as a Non-active Site Inhibitor of Protozoal Bifunctional Thymidylate Synthase-Dihydrofolate Reductase*

I. Coppens, J. Irwin, B. Shoichet, 2003, The Journal of Biological Chemistry.

Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities

Brian K. Shoichet, David B. Goodin, Marcus Fischer, 2013, PloS one.

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

Miguel Correa Marrero, Robyn M. Kaake, Gwendolyn M. Jang, 2020, Science.

Interaction energies between β‐lactam antibiotics and E. coli penicillin‐binding protein 5 by reversible thermal denaturation

B. Shoichet, B. Beadle, R. Nicholas, 2001, Protein science : a publication of the Protein Society.

The activities of drug inactive ingredients on biological targets

Samuel T. Slocum, E. Berg, J. Irwin, 2020, Science.

FOR THE RECORD Re-examining the role of Lys67 in class C b-lactamase catalysis

B. Shoichet, A. McReynolds, 2009 .

Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M β-Lactamases

B. Shoichet, R. Bonnet, Yu Chen, 2007 .

Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP.

B. Shoichet, K. Giacomini, Natalia Khuri, 2020, Molecular pharmaceutics.

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.

J. Irwin, B. Shoichet, J. Taunton, 2019, Journal of the American Chemical Society.

Structure-based discovery of conformationally selective inhibitors of the serotonin transporter

B. Shoichet, A. Basbaum, R. Rodriguiz, 2022, Cell.

Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2

Yurii S. Moroz, J. Irwin, B. Shoichet, 2022, bioRxiv.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

Trey Ideker, Claudia Hernandez-Armenta, Brian K. Shoichet, 2020, bioRxiv.

The Impact of Introducing a Histidine into an Apolar Cavity Site on Docking and Ligand Recognition

B. Shoichet, M. Merski, 2013, Journal of medicinal chemistry.

Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors

Yurii S. Moroz, J. Irwin, B. Shoichet, 2022, bioRxiv.

Inactive and active state structures template selective tools for the human 5-HT5A receptor

B. Shoichet, B. Roth, V. Katritch, 2022, Nature Structural & Molecular Biology.

Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor

Yurii S. Moroz, J. Irwin, B. Shoichet, 2022, Science.

Computational biology and high performance computing

Brian K. Shoichet, Adam P. Arkin, Horst D. Simon, 1999 .

Quantitative and Systems Pharmacology in the Post-genomic Era : New Approaches to Discovering Drugs and Understanding Therapeutic

Ravi Iyengar, Darrell R. Abernethy, Paolo Vicini, 2011 .

Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity

Samuel T. Slocum, J. Irwin, B. Shoichet, 2022, Nature.

Docking for fragment inhibitors of AmpC (cid:1) -lactamase

B. Shoichet, R. S. Ferreira, G. Rocklin, 2009 .

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

Yurii S. Moroz, J. Irwin, B. Shoichet, 2022, bioRxiv.

Rapid behavior—based identification of neuroactive small molecules in the zebrafish

Christian Laggner, Stephen J. Haggarty, Brian Shoichet, 2009, Nature chemical biology.

Modeling the expansion of virtual screening libraries

J. Irwin, B. Shoichet, Jiankun Lyu, 2023, Nature Chemical Biology.

A Crowding Barrier to Protein Inhibition in Colloidal Aggregates.

B. Shoichet, M. Jacobson, Xuewen Du, 2021, Journal of medicinal chemistry.

Ligand recognition and allosteric modulation of the human MRGPRX1 receptor

B. Shoichet, Xi-Ping Huang, B. Roth, 2022, Nature Chemical Biology.

Functional analyses of AmpC β‐lactamase through differential stability

B. Shoichet, S. McGovern, A. Patera, 1999 .

Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2

Matthew J. O’Meara, N. Krogan, M. Vignuzzi, 2021, Science.

Docking a bespoke ultra-large tetrahydropyridine library identifies 5-HT2A receptor agonists conferring new biology

Samuel T. Slocum, J. Irwin, B. Shoichet, 2022 .

Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2

R. Andino, B. Shoichet, X. Shu, 2023, Nature Microbiology.

Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as β-lactamase inhibitors.

Fabio Prati, Richard Bonnet, Kerim Babaoglu, 2010, Journal of medicinal chemistry.

Here Be Dragons: Docking and Screening in an Uncharted Region of Chemical Space

John J Irwin, Brian K Shoichet, Ruth Brenk, 2005, Journal of biomolecular screening.

Structure-based approach for binding site identification on AmpC beta-lactamase.

Brian K Shoichet, B. Shoichet, Rachel A Powers, 2002, Journal of medicinal chemistry.

Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .

B. Shoichet, A. Fedorov, E. Fedorov, 2010, Biochemistry.

Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors.

Kristin E. D. Coan, Brian K Shoichet, B. Shoichet, 2008, Journal of the American Chemical Society.

Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures.

Brian K Shoichet, B. Shoichet, Brian Y Feng, 2006, Journal of medicinal chemistry.

Virtual Screening in Drug Discovery

Brian K. Shoichet, Juan Alvarez, B. Shoichet, 2005 .

Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors.

B. Shoichet, E. Caselli, F. Prati, 2008, Bioorganic & medicinal chemistry.

The promise and peril of chemical probes.

John P. Overington, Jian Jin, Matthieu Schapira, 2015, Nature chemical biology.

Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.

B. Shoichet, Shih‐Yuan Liu, M. Fischer, 2016, Journal of the American Chemical Society.

An extended-spectrum AmpC-type beta-lactamase obtained by in vitro antibiotic selection.

B. Shoichet, F. Baquero, M. Negri, 1998, FEMS microbiology letters.

Structure and Dynamics of CTX-M Enzymes Reveal Insights into Substrate Accommodation by Extended-spectrum β-Lactamases

B. Shoichet, R. Bonnet, Yu Chen, 2008 .

Erratum: The promise and peril of chemical probes (Nature Chemical Biology (2015) 11 (536-541))

John P. Overington, Jayme L. Dahlin, Christopher M. Austin, 2015 .

The Structural Bases of Antibiotic Resistance in the Clinically Derived Mutant β-Lactamases TEM-30, TEM-32, and TEM-34*

Brian K Shoichet, B. Shoichet, G. Minasov, 2002, The Journal of Biological Chemistry.

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

Brian K. Shoichet, John J. Irwin, J. Irwin, 2005, J. Chem. Inf. Model..

Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents.

Nir London, Katrina T Forest, Brian K Shoichet, 2015, ACS chemical biology.

Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.

B. Shoichet, A. Fedorov, E. Fedorov, 2012, Biochemistry.

Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.

A. Sali, B. Shoichet, Hao Fan, 2013, Biochemistry.

Structure-based design of a chemical probe set for the 5-HT5A serotonin receptor

Samuel T. Slocum, Ryan T. Strachan, B. Shoichet, 2021, bioRxiv.

STRUCTURE OF THE D2 DOPAMINE RECEPTOR BOUND TO THE ATYPICAL ANTIPSYCHOTIC DRUG RISPERIDONE

Anat Levit, Bryan L. Roth, Brian K. Shoichet, 2018, Nature.

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

Xin Chen, Sheng Wang, Jian Jin, 2015, Nature.

Molecular docking using shape descriptors

Brian K. Shoichet, Irwin D. Kuntz, Dale L. Bodian, 1992 .

The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

Brian K. Shoichet, Ryan G. Coleman, James S. Fraser, 2014, Nature chemistry.

Virtual screening of chemical libraries

Brian K. Shoichet, B. Shoichet, 2004, Nature.

A chemical screen identifies class a g-protein coupled receptors as regulators of cilia.

B. Shoichet, W. Marshall, Elisabet Gregori-Puigjané, 2012, ACS chemical biology.

Actin Is Required for IFT Regulation in Chlamydomonas reinhardtii

B. Shoichet, W. Marshall, W. Sale, 2014, Current Biology.

Small-molecule aggregates inhibit amyloid polymerization.

Jonathan Weissman, David W. Colby, Brian K Shoichet, 2008, Nature chemical biology.

Structures of the σ2 receptor enable docking for bioactive ligand discovery

Yurii S. Moroz, Matthew J. O’Meara, J. Irwin, 2021, Nature.

Crystal structures of the σ2 receptor template large-library docking for selective chemotypes active in vivo

Yurii S. Moroz, Matthew J. O’Meara, J. Irwin, 2021, bioRxiv.

Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor.

Samuel T. Slocum, Ryan T. Strachan, B. Shoichet, 2022, Journal of medicinal chemistry.

A practical guide to large-scale docking

Reed M. Stein, J. Irwin, B. Shoichet, 2021, Nature Protocols.

Ligand Strain Energy in Large Library Docking

Matthew S. Smith, J. Irwin, B. Shoichet, 2021, bioRxiv.

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

John D. McCorvy, Bryan L. Roth, Brian K. Shoichet, 2020, Nature.

Structure-based discovery of opioid analgesics with reduced side effects

Henry Lin, Grégory Scherrer, Aashish Manglik, 2016, Nature.

Ligand Pose and Orientational Sampling in Molecular Docking

Brian K. Shoichet, Ryan G. Coleman, John J. Irwin, 2013, PloS one.

Structure-based ligand discovery for the protein–protein interface of chemokine receptor CXCR4

Michael M. Mysinger, Dahlia R. Weiss, Brian K Shoichet, 2012, Proceedings of the National Academy of Sciences.

Structure-based discovery of β2-adrenergic receptor ligands

Peter Kolb, Brian K. Kobilka, Brian K. Shoichet, 2009, Proceedings of the National Academy of Sciences.

Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7-methyltransferase

Yurii S. Moroz, J. Irwin, B. Shoichet, 2023, bioRxiv.

Structural identification of a hotspot on CFTR for potentiation

B. Shoichet, A. Levit, Jue Chen, 2019, Science.

Structural bases for stability-function tradeoffs in antibiotic resistance.

B. Shoichet, V. Thomas, A. McReynolds, 2010, Journal of molecular biology.

Testing inhomogeneous solvation theory in structure-based ligand discovery

Michael K Gilson, Tom Kurtzman, Brian K Shoichet, 2017, Proceedings of the National Academy of Sciences.

Stability for function trade-offs in the enolase superfamily "catalytic module".

Patricia C Babbitt, Brian K Shoichet, P. Babbitt, 2007, Biochemistry.

Allosteric inhibition through core disruption.

James R Horn, Brian K Shoichet, B. Shoichet, 2004, Journal of molecular biology.

Large-scale identification and analysis of suppressive drug interactions.

Murodzhon Akhmedov, Raul Rodriguez-Esteban, Corey Nislow, 2014, Chemistry & biology.

Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives

B. Shoichet, P. Turnbaugh, K. Giacomini, 2019, Proceedings of the National Academy of Sciences.

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites

B. Shoichet, J. Fraser, M. Fischer, 2015, Chembiochem : a European journal of chemical biology.

Prediction of enzymatic pathways by integrative pathway mapping

Henry Lin, Andrej Sali, Matthew P Jacobson, 2018, eLife.

Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens.

B. Shoichet, C. Craik, Tia A. Tummino, 2021, Journal of medicinal chemistry.

Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions

Brian K. Shoichet, Andrej Sali, Guang Qiang Dong, 2011, J. Chem. Inf. Model..

Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.

R Abagyan, I D Kuntz, M Sternberg, 1996, Nature structural biology.

Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design.

G S Weston, S J Remington, B K Shoichet, 1998, Biochemistry.

GAIN domain–mediated cleavage is required for activation of G protein–coupled receptor 56 (GPR56) by its natural ligands and a small-molecule agonist

B. Shoichet, K. Monk, P. Lak, 2019, The Journal of Biological Chemistry.

Far away from the lamppost

Avi Ma'ayan, Stephan Schürer, Michael T. McManus, 2018, PLoS biology.

Internal Structure and Preferential Protein Binding of Colloidal Aggregates.

D. Elnatan, B. Shoichet, D. Agard, 2017, ACS chemical biology.

Colloidal Aggregation Affects the Efficacy of Anticancer Drugs in Cell Culture

B. Shoichet, Allison K. Doak, Pascal Wassam, 2012, ACS chemical biology.

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

A. Ashworth, J. Irwin, B. Shoichet, 2021, Science Advances.

Structure-Based Discovery of a Novel, Noncovalent Inhibitor of AmpC β-Lactamase

Brian K. Shoichet, B. Shoichet, Federica Morandi, 2002 .

Sara Ballouz, Jesse Gillis, Matthew J O'Meara, 2016, PloS one.

Structure-Based Discovery of a Novel , Noncovalent Inhibitor of AmpC-Lactamase tors

B. Shoichet, F. Morandi, 2002 .

Structure-based design and in-parallel synthesis of inhibitors of AmpC β-lactamase

Maria Paola Costi, B. Shoichet, E. Caselli, 2001 .

Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.

B. Shoichet, E. Caselli, F. Prati, 2001, Chemistry & biology.

Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.

B. Shoichet, M. Shoichet, C. K. McLaughlin, 2016, ACS chemical biology.

The Presynaptic Component of the Serotonergic System is Required for Clozapine's Efficacy

Michael J. Keiser, Bryan L Roth, John J Irwin, 2011, Neuropsychopharmacology.

Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily.

Sugadev Ragumani, Magdalena Korczynska, Brian K Shoichet, 2013, Biochemistry.

Functional Annotation and Three-Dimensional Structure of an Incorrectly Annotated Dihydroorotase from cog 3964 in the Amidohydrolase Superfamily Argentina

B. Shoichet, F. Raushel, S. Swaminathan, 2012 .

Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB.

Christopher P Austin, Anton Simeonov, James Inglese, 2010, Journal of medicinal chemistry.

Structure-Based Optimization of a Non-β-lactam Lead Results in Inhibitors That Do Not Up-Regulate β-Lactamase Expression in Cell Culture

Maria Paola Costi, Donatella Tondi, Richard Bonnet, 2005 .

Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy.

Giuseppe Cannazza, Maria Paola Costi, Donatella Tondi, 2007, Journal of medicinal chemistry.

The complexed structure and antimicrobial activity of a non‐β‐lactam inhibitor of AmpC β‐lactamase

Jesús Blázquez, Fernando Baquero, B. Shoichet, 2008, Protein science : a publication of the Protein Society.

The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.

B. Shoichet, G. Minasov, Tomer A. Roth, 2006, Journal of the American Chemical Society.

Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design.

B K Shoichet, B. Shoichet, E. Caselli, 2001, Biochemistry.

Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase.

Brian K Shoichet, B. Shoichet, D. Golemi-Kotra, 2005, Biochemistry.

Re‐examining the role of Lys67 in class C β‐lactamase catalysis

Brian K Shoichet, B. Shoichet, Yu Chen, 2009, Protein science : a publication of the Protein Society.

Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.

Beth M Beadle, Brian K Shoichet, B. Shoichet, 2002, Structure.

Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.

Brian K. Shoichet, Maria Paola Costi, Donatella Tondi, 2010, Bioorganic & medicinal chemistry letters.

Structure-based design and in-parallel synthesis of inhibitors of AmpC L-lactamase

B. Shoichet, E. Caselli, M. Negri, 2001 .

Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2

Matthew J. O’Meara, N. Krogan, M. Vignuzzi, 2021, bioRxiv.

Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease.

Christopher P Austin, Anton Simeonov, James Inglese, 2010, Journal of medicinal chemistry.

Stability and equilibria of promiscuous aggregates in high protein milieus.

Kristin E. D. Coan, Brian K Shoichet, B. Shoichet, 2007, Molecular bioSystems.

Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase.

Jian Wang, Timothy Palzkill, Brian K Shoichet, 2008, Journal of molecular biology.

Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase.

Jian Wang, Brian K. Shoichet, Timothy Palzkill, 2008, Journal of molecular biology.

Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture.

Maria Paola Costi, Donatella Tondi, Richard Bonnet, 2005, Journal of the American Chemical Society.

Covalent Docking of Large Libraries for the Discovery of Chemical Probes

Nir London, Brian K. Shoichet, Kenji Uchida, 2014, Nature chemical biology.

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

Brian K. Shoichet, John J. Irwin, Gregg Siegal, 2014, ACS chemical biology.

O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site.

Pauline N. Wyrembak, B. Shoichet, R. Pratt, 2007, Journal of the American Chemical Society.

Thermodynamic cycle analysis and inhibitor design against beta-lactamase.

B. Shoichet, G. Minasov, Tomer A. Roth, 2003, Biochemistry.

Nanomolar inhibitors of AmpC beta-lactamase.

B. Shoichet, E. Caselli, P. Focia, 2003, Journal of the American Chemical Society.

Structural Basis for Imipenem Inhibition of Class C β-Lactamases

B. Shoichet, B. Beadle, 2002, Antimicrobial Agents and Chemotherapy.

Using steric hindrance to design new inhibitors of class C beta-lactamases.

Brian K Shoichet, B. Shoichet, Indi Trehan, 2002, Chemistry & biology.

Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.

B. Shoichet, B. Beadle, Indi Trehan, 2001, Biochemistry.

Crystal Structures of Substrate and Inhibitor Complexes with AmpC β-Lactamase: Possible Implications for Substrate-Assisted Catalysis

B. Shoichet, L. Blaszczak, A. Patera, 2000 .

Nanomolar Inhibitors of AmpC â-Lactamase

B. Shoichet, E. Caselli, P. Focia, 2022 .

Structure-based design and solid phase synthesis of novel AmpC b-lactamase inhibitors

B. Shoichet, E. Caselli, M. Costi, 2001 .

Prediction and validation of enzyme and transporter off-targets for metformin

Michael J. Keiser, B. Shoichet, K. Giacomini, 2015, Journal of Pharmacokinetics and Pharmacodynamics.

Structure-based Inhibitor Discovery against Adenylyl Cyclase Toxins from Pathogenic Bacteria That Cause Anthrax and Whooping Cough*

Brian K. Shoichet, Milan Mrksich, Yuequan Shen, 2003, Journal of Biological Chemistry.

Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion.

B. Shoichet, D. Santi, P. Balaram, 1994, Biochemistry.

Structure, function and pharmacology of human itch GPCRs

Reid H. J. Olsen, Samuel T. Slocum, L. Jan, 2021, Nature.

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

David L Mobley, Ken A Dill, Alan P Graves, 2009, Journal of molecular biology.

Isolation and characterization of multiple-methionine mutants of T4 lysozyme with simplified cores

B. Matthews, B. Shoichet, W. Baase, 1997 .

A New Spin on Antibody-Drug Conjugates: Trastuzumab-Fulvestrant Colloidal Drug Aggregates Target HER2-Positive Cells.

B. Shoichet, M. Shoichet, C. K. McLaughlin, 2017, ACS applied materials & interfaces.

Structure-based discovery of cannabinoid-1 receptor agonists with reduced side effects

Yurii S. Moroz, Reed M. Stein, J. Irwin, 2023, bioRxiv.

Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases.

Richard Bonnet, Brian Shoichet, B. Shoichet, 2005, Journal of the American Chemical Society.

The hunt for 8-oxoguanine deaminase.

Peter Kolb, Stephen K. Burley, Brian K. Shoichet, 2010, Journal of the American Chemical Society.

Drug discovery: nature's pieces.

B. Shoichet, Brian K. Shoichet, 2013, Nature chemistry.

Efficient Exploration of Chemical Space with Docking and Deep Learning.

Robert Abel, Matthew P. Repasky, Y Yang, 2021, Journal of chemical theory and computation.

Property-Unmatched Decoys in Docking Benchmarks

Brian K. Shoichet, John J. Irwin, Trent E. Balius, 2021, J. Chem. Inf. Model..

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

Yurii S. Moroz, J. Irwin, B. Shoichet, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens

B. Shoichet, C. Craik, Tia A. Tummino, 2021, bioRxiv.

Covalent Docking Predicts Substrates for Haloalkanoate Dehalogenase Superfamily Phosphatases

Nir London, Patricia C. Babbitt, Brian K. Shoichet, 2014, Biochemistry.

Noncovalent interaction energies in covalent complexes: TEM‐1 β‐lactamase and β‐lactams

B. Shoichet, G. Minasov, Xiao-ju Wang, 2002 .

Molecular Docking Screens Using Comparative Models of Proteins

Gerhard Klebe, Brian K. Shoichet, Andrej Sali, 2009, J. Chem. Inf. Model..

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.

Elisabet Gregori-Puigjané, Udo Oppermann, Anthony Tumber, 2016, Journal of medicinal chemistry.

Predicting the structure of protein complexes: a step in the right direction.

I D Kuntz, B K Shoichet, I. Kuntz, 1996, Chemistry & biology.

Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists

B. Shoichet, R. Sunahara, B. Kobilka, 2018, Proceedings of the National Academy of Sciences.

Colloidal aggregation and the in vitro activity of traditional Chinese medicines.

B. Shoichet, Allison K. Doak, L. Nedyalkova, 2015, ACS chemical biology.

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

Robyn M. Kaake, Gwendolyn M. Jang, Matthew J. O’Meara, 2020, Nature.

Targeting Class A and C Serine β-Lactamases with a Broad-Spectrum Boronic Acid Derivative

Maria Paola Costi, B. Shoichet, R. Bonnet, 2014, Journal of medicinal chemistry.

Synthetic Ionizable Colloidal Drug Aggregates Enable Endosomal Disruption

B. Shoichet, M. Shoichet, M. Lautens, 2023, Advanced science.

Triggered Release Enhances the Cytotoxicity of Stable Colloidal Drug Aggregates.

B. Shoichet, M. Shoichet, P. Lak, 2019, ACS chemical biology.

Colloidal Drug Aggregate Stability in High Serum Conditions and Pharmacokinetic Consequence.

B. Shoichet, R. Al-awar, M. Shoichet, 2019, ACS chemical biology.

Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations.

B. Shoichet, M. Shoichet, T. Koch, 2017, Molecular pharmaceutics.

Design, Synthesis, and Biological Evaluation of Novel Tetrahydroprotoberberine Derivatives (THPBs) as Selective α1A-Adrenoceptor Antagonists.

Hualiang Jiang, B. Shoichet, Honglin Li, 2016, Journal of medicinal chemistry.

Design , Synthesis , and Biological Evaluation of Novel Tetrahydroprotoberberine Derivatives ( THPBs ) as Selective α 1 A-Adrenoceptor Antagonists

Hualiang Jiang, B. Shoichet, Honglin Li, 2016 .

D4 dopamine receptor high-resolution structures enable the discovery of selective agonists

Anat Levit, Ron O Dror, Bryan L Roth, 2017, Science.

An allosteric modulator binds to a conformational hub in the β2 adrenergic receptor

B. Shoichet, R. Sunahara, B. Kobilka, 2020, Nature Chemical Biology.

Crystal structures of penicillin-binding protein 6 from Escherichia coli.

B. Shoichet, S. Mobashery, Yu Chen, 2009, Journal of the American Chemical Society.

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

Kenny K H Ang, Adam R Renslo, Brian K Shoichet, 2009, Journal of medicinal chemistry.

Quantifying the Relationships among Drug Classes

Tudor I. Oprea, Jérôme Hert, Brian K. Shoichet, 2008, J. Chem. Inf. Model..

Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1 B

Brian K. Shoichet, Thompson N. Doman, Daniel T. Connolly, 2022 .

Muscarinic Receptors as Model Targets and Antitargets for Structure-Based Ligand Discovery

Peter Gmeiner, Dahlia R. Weiss, Brian K Shoichet, 2013, Molecular Pharmacology.

In Silico Molecular Comparisons of C. elegans and Mammalian Pharmacology Identify Distinct Targets That Regulate Feeding

Maria F. Sassano, Bryan L. Roth, Brian K. Shoichet, 2013, PLoS biology.

Identification of a conserved drug binding pocket in TMEM16 proteins

Y. Jan, L. Jan, B. Shoichet, 2022, Research square.

Structure, function and pharmacology of human itch GPCRs

Reid H. J. Olsen, Samuel T. Slocum, B. Shoichet, 2021, Nature.

Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.

B. Shoichet, D. Agard, J. Rubinstein, 2015, ACS chemical biology.

Structure-Based Discovery of A2A Adenosine Receptor Ligands

Brian K. Shoichet, John J. Irwin, Jens Carlsson, 2010, Journal of medicinal chemistry.

Structure-guided discovery of new deaminase enzymes.

Daniel S. Hitchcock, A. Sali, B. Shoichet, 2013, Journal of the American Chemical Society.

Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.

Andrej Sali, Daniel S. Hitchcock, Steven C Almo, 2013, Journal of the American Chemical Society.

Prediction of Substrates for Glutathione Transferases by Covalent Docking

Richard N. Armstrong, Patricia C. Babbitt, Brian K. Shoichet, 2014, J. Chem. Inf. Model..

Energy penalties enhance flexible receptor docking in a model cavity

B. Shoichet, T. E. Balius, I. Singh, 2021, Proceedings of the National Academy of Sciences.

Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily.

B. Shoichet, A. Fedorov, S. Almo, 2009, Biochemistry.

Differential roles of extracellular Histidine residues of GPR68 for proton-sensing and allosteric modulation by divalent metal ions.

B. Shoichet, Xi-Ping Huang, B. Roth, 2020, Biochemistry.

Drug discovery: follow your lead.

B. Shoichet, 2014, Nature chemical biology.

Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward.

Jürgen Bajorath, W. Patrick Walters, Brian K. Shoichet, 2016, Journal of medicinal chemistry.

Engineering a model protein cavity to catalyze the Kemp elimination

Brian K Shoichet, B. Shoichet, M. Merski, 2012, Proceedings of the National Academy of Sciences.

Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.

B. Shoichet, G. Minasov, Xiaojun Wang, 2002, Proteins.

Profiling the diversity of agonist-selective effects on the proximal proteome environment of G protein-coupled receptors

Benjamin J. Polacco, N. Krogan, B. Shoichet, 2022, bioRxiv.

Thermodynamic prediction of protein neutrality.

C. Wilke, C. Adami, F. Arnold, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Prediction of enzymatic pathways by integrative pathway mapping

Matthew J. O’Meara, Daniel Russel, A. Sali, 2018, eLife.

Functional Annotation and Structural Characterization of a Novel Lactonase Hydrolyzing d-Xylono-1,4-lactone-5-phosphate and l-Arabino-1,4-lactone-5-phosphate

Peter Kolb, Stephen K. Burley, Brian K. Shoichet, 2014, Biochemistry.

Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.

Michael J. Keiser, B. Shoichet, A. Degraw, 2010, Journal of medicinal chemistry.

Docking Screens for Novel Ligands Conferring New Biology.

J. Irwin, B. Shoichet, 2016, Journal of medicinal chemistry.

Predicting new molecular targets for known drugs

Michael J. Keiser, J. Irwin, B. Shoichet, 2009, Nature.

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

B. Shoichet, R. S. Ferreira, A. Renslo, 2009, Journal of Medicinal Chemistry.

Kinase inhibitors: not just for kinases anymore.

B. Shoichet, S. McGovern, 2003, Journal of medicinal chemistry.

An Aggregation Advisor for Ligand Discovery.

J. Irwin, B. Shoichet, Allison K. Doak, 2015, Journal of medicinal chemistry.

Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.

A. Sali, B. Shoichet, Hao Fan, 2013, Biochemistry.

Structure-guided discovery of new deaminase enzymes.

Daniel S. Hitchcock, A. Sali, B. Shoichet, 2013, Journal of the American Chemical Society.

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.

J. Irwin, B. Shoichet, J. Taunton, 2019, Journal of the American Chemical Society.

A Molecular Basis for Innovation in Drug Excipients

R Lionberger, K M Giacomini, J J Irwin, 2017, Clinical pharmacology and therapeutics.

Muscarinic Receptors as Model Targets and Antitargets for Structure-Based Ligand Discovery

Dahlia R. Weiss, J. Wess, B. Shoichet, 2013, Molecular Pharmacology.

The Enzyme Function Initiative.

Heidi J. Imker, A. Sali, P. Babbitt, 2011, Biochemistry.

Discovery of a functionally selective serotonin 5-HT1A receptor agonist for the treatment of pain

B. Shoichet, A. Inoue, J. Braz, 2023, bioRxiv.

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

Viktoriya D. Nikolova, Kara A. Saddoris, B. Shoichet, 2015, Nature.

Colloidal aggregation: from screening nuisance to formulation nuance.

B. Shoichet, M. Shoichet, Ahil N. Ganesh, 2018, Nano today.

A Survey of Antiprion Compounds Reveals the Prevalence of Non-PrP Molecular Targets*

S. Prusiner, B. Shoichet, G. Poncet-Montange, 2011, The Journal of Biological Chemistry.

A chemical screen identifies class a g-protein coupled receptors as regulators of cilia.

B. Shoichet, W. Marshall, Elisabet Gregori-Puigjané, 2012, ACS Chemical Biology.

The promise and peril of chemical probes (vol 11, pg 536, 2015)

John P. Overington, Jayme L. Dahlin, Christopher M. Austin, 2015 .

Drug discovery: nature's pieces.

B. Shoichet, 2013, Nature Chemistry.

Blind prediction of charged ligand binding affinities in a model binding site.

K. Dill, D. Mobley, B. Shoichet, 2013, Journal of molecular biology.

Large library docking for novel SARS‐CoV‐2 main protease non‐covalent and covalent inhibitors

Yurii S. Moroz, J. Irwin, B. Shoichet, 2023, Protein science : a publication of the Protein Society.

Here Be Dragons: Docking and Screening in an Uncharted Region of Chemical Space

J. Irwin, B. Shoichet, R. Brenk, 2005, Journal of biomolecular screening.

Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor

J. Irwin, B. Shoichet, Jiankun Lyu, 2023, bioRxiv.

Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs

Kyle V. Butler, R. Dror, B. Shoichet, 2017, Nature chemical biology.