List of works - Brian K. Shoichet

A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening

scientific article

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

scientific article published on 20 March 2017

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

scientific article published on 30 April 2020

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

journal article from 'bioRxiv' published in 2020

A model binding site for testing scoring functions in molecular docking

scientific article

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

scientific article published on 01 June 2020

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

scientific article

Benchmarking sets for molecular docking

scientific article (publication date: 16 November 2006)

Chemical informatics and target identification in a zebrafish phenotypic screen.

scientific article published on 18 December 2011

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

scientific article

Colloidal Drug Aggregate Stability in High Serum Conditions and Pharmacokinetic Consequence

scientific article published on 12 March 2019

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

scientific article published on 15 October 2020

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

scientific article

Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against β-Lactamase

scientific article

Covalent docking of large libraries for the discovery of chemical probes

scientific article

Crystal Structures of Penicillin-Binding Protein 6 from Escherichia coli

scientific article

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

scientific article

Differential Roles of Extracellular Histidine Residues of GPR68 for Proton-Sensing and Allosteric Modulation by Divalent Metal Ions

scientific article published on 10 September 2020

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking

scientific article published on 04 March 2020

Docking Screens for Novel Ligands Conferring New Biology

scientific article

Docking and chemoinformatic screens for new ligands and targets

scientific article published on August 2009

Docking for fragment inhibitors of AmpC -lactamase

scientific article

Efficient Exploration of Chemical Space with Docking and Deep Learning

scientific article published on 30 September 2021

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

scientific article

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

scientific article published on 24 November 2020

Functional Annotation and Three-Dimensional Structure of Dr0930 from Deinococcus radiodurans , a Close Relative of Phosphotriesterase in the Amidohydrolase Superfamily † ‡

scientific article

Genetic and Structural Characterization of an L201P Global Suppressor Substitution in TEM-1 β-Lactamase

scientific article

Here be dragons: docking and screening in an uncharted region of chemical space

scientific article published on 16 September 2005

Hierarchical docking of databases of multiple ligand conformations

scientific article

Identification and Optimization of Inhibitors of Trypanosomal Cysteine Proteases: Cruzain, Rhodesain, and TbCatB

scientific article

Identification of Novel Smoothened Ligands Using Structure-Based Docking

scientific article

In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding

scientific article (publication date: November 2013)

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

scientific article

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

scientific article published on 10 February 2020

Internal Structure and Preferential Protein Binding of Colloidal Aggregates.

scientific article published on 16 December 2016

Lead discovery using molecular docking

scientific article

Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations.

scientific article

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

scientific article

Ligand pose and orientational sampling in molecular docking

scientific article (publication date: 2013)

Molecular docking and ligand specificity in fragment-based inhibitor discovery

scientific article

Molecular docking screens using comparative models of proteins

scientific article

Nanomolar inhibitors of AmpC beta-lactamase

scientific article

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

scientific article

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

scientific article

Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy

scientific article

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

scientific article

Predicting absolute ligand binding free energies to a simple model site

scientific article

Predicting new molecular targets for known drugs

scientific article

Prediction of enzymatic pathways by integrative pathway mapping.

scientific article

Protein Stability Effects in Aggregate-Based Enzyme Inhibition

scientific article published on 17 October 2019

Quantifying biogenic bias in screening libraries

scientific article

Quantifying the relationships among drug classes

scientific article published on 13 March 2008

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

scientific article

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

scientific article

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

scientific article

Recognition and resistance in TEM beta-lactamase

scientific article

Relating protein pharmacology by ligand chemistry

scientific article (publication date: February 2007)

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

scientific article

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

scientific article

Statistical potential for modeling and ranking of protein-ligand interactions

scientific article published on 21 November 2011

Structural Bases for Stability–Function Tradeoffs in Antibiotic Resistance

scientific article

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

scientific article

Structural bases of stability-function tradeoffs in enzymes

scientific article

Structural basis for imipenem inhibition of class C beta-lactamases

scientific article

Structural identification of a hotspot on CFTR for potentiation

scientific article

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

scientific article

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

scientific article

Structure, Mechanism, and Substrate Profile for Sco3058: The Closest Bacterial Homologue to Human Renal Dipeptidase,

scientific article

Structure, function and pharmacology of human itch GPCRs

scientific article published on 17 November 2021

Structure-Based Design and Discovery of New M2 Receptor Agonists

scientific article published on 2 November 2017

Structure-based activity prediction for an enzyme of unknown function

scientific article

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

scientific article

Structure-based discovery of A2A adenosine receptor ligands

scientific article

Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase

scientific article

Structure-based discovery of antagonists of nuclear receptor LRH-1.

scientific article published on 10 May 2013

Structure-based discovery of beta2-adrenergic receptor ligands

scientific article

Structure-based discovery of opioid analgesics with reduced side effects

scientific article

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

scientific article

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

scientific article

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

scientific article

The Enzyme Function Initiative

scientific article

The Hunt for 8-Oxoguanine Deaminase

scientific article

The activities of drug inactive ingredients on biological targets

scientific article

The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34

scientific article

Thermodynamic cycle analysis and inhibitor design against beta-lactamase

scientific article

Triggered Release Enhances the Cytotoxicity of Stable Colloidal Drug Aggregates

scientific article published on 25 June 2019

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

scientific article

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

scientific article (publication date: 16 October 2015)

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

scientific article published on 10 February 2020

ZINC--a free database of commercially available compounds for virtual screening

scientific article

List of works by Brian K. Shoichet

A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening

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

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

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

A model binding site for testing scoring functions in molecular docking

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

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

Benchmarking sets for molecular docking

Chemical informatics and target identification in a zebrafish phenotypic screen.

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

Colloidal Drug Aggregate Stability in High Serum Conditions and Pharmacokinetic Consequence

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

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

Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against β-Lactamase

Covalent docking of large libraries for the discovery of chemical probes

Crystal Structures of Penicillin-Binding Protein 6 from Escherichia coli

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

Differential Roles of Extracellular Histidine Residues of GPR68 for Proton-Sensing and Allosteric Modulation by Divalent Metal Ions

Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking

Docking Screens for Novel Ligands Conferring New Biology

Docking and chemoinformatic screens for new ligands and targets

Docking for fragment inhibitors of AmpC -lactamase

Efficient Exploration of Chemical Space with Docking and Deep Learning

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

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

Functional Annotation and Three-Dimensional Structure of Dr0930 from Deinococcus radiodurans , a Close Relative of Phosphotriesterase in the Amidohydrolase Superfamily † ‡

Genetic and Structural Characterization of an L201P Global Suppressor Substitution in TEM-1 β-Lactamase

Here be dragons: docking and screening in an uncharted region of chemical space

Hierarchical docking of databases of multiple ligand conformations

Identification and Optimization of Inhibitors of Trypanosomal Cysteine Proteases: Cruzain, Rhodesain, and TbCatB

Identification of Novel Smoothened Ligands Using Structure-Based Docking

In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

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

Internal Structure and Preferential Protein Binding of Colloidal Aggregates.

Lead discovery using molecular docking

Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations.

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

Ligand pose and orientational sampling in molecular docking

Molecular docking and ligand specificity in fragment-based inhibitor discovery

Molecular docking screens using comparative models of proteins

Nanomolar inhibitors of AmpC beta-lactamase

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

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

Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

Predicting absolute ligand binding free energies to a simple model site

Predicting new molecular targets for known drugs

Prediction of enzymatic pathways by integrative pathway mapping.

Protein Stability Effects in Aggregate-Based Enzyme Inhibition

Quantifying biogenic bias in screening libraries

Quantifying the relationships among drug classes

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

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

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

Recognition and resistance in TEM beta-lactamase

Relating protein pharmacology by ligand chemistry

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

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

Statistical potential for modeling and ranking of protein-ligand interactions

Structural Bases for Stability–Function Tradeoffs in Antibiotic Resistance

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

Structural bases of stability-function tradeoffs in enzymes

Structural basis for imipenem inhibition of class C beta-lactamases

Structural identification of a hotspot on CFTR for potentiation

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

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

Structure, Mechanism, and Substrate Profile for Sco3058: The Closest Bacterial Homologue to Human Renal Dipeptidase,

Structure, function and pharmacology of human itch GPCRs

Structure-Based Design and Discovery of New M2 Receptor Agonists

Structure-based activity prediction for an enzyme of unknown function

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

Structure-based discovery of A2A adenosine receptor ligands

Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase

Structure-based discovery of antagonists of nuclear receptor LRH-1.

Structure-based discovery of beta2-adrenergic receptor ligands

Structure-based discovery of opioid analgesics with reduced side effects

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

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