Brian Shoichet, PhD
Professor
Pharmaceutical Chemistry
School of Pharmacy

Applying these to G-Protein Coupled Receptors (GPCRs), which are the single largest family of signaling receptors in human cells.

Allied with this effort is an experimental research program that 3. Tests the new methods in well-controlled systems, determining x-ray crystal structures and measuring binding thermodynamics. The experimental program has led to unexpected discoveries, including the observation that many drugs and reagents can form colloidal aggregates in solution. This has led us to investigate 4. How the physical organic chemistry of drugs affects their behavior in vitro and in vivo, influencing drug delivery and formulation.

A new effort turns the entire structural view on its head, 5. Developing computational methods to relate receptors by the similarity of their ligands, rather than by protein sequence or structure. This changes pharmacological relationships dramatically—targets that would normally be considered sequence neighbors are pushed far apart (because their ligands are dissimilar), whereas other targets that supposedly have nothing to do with one another become neighbors (because their ligands are very similar). Since the new relationships are articulated by ligands, they may be directly tested both on isolated receptors and, increasingly, against model whole organisms, such as zebra fish, C. elegans and mice. This project seeks to discover the integrated chemical circuits through which drugs and reagents affect whole organisms. "

• AlphaFold2 structures template ligand discovery.
  bioRxiv : the preprint server for biology 2023 Lyu J, Kapolka N, Gumpper R, Alon A, Wang L, Jain MK, Barros-Álvarez X, Sakamoto K, Kim Y, DiBerto J, Kim K, Tummino TA, Huang S, Irwin JJ, Tarkhanova OO, Moroz Y, Skiniotis G, Kruse AC, Shoichet BK, …
• Docking for EP4R antagonists active against inflammatory pain.
  Nature communications 2023 Gahbauer S, DeLeon C, Braz JM, Craik V, Kang HJ, Wan X, Huang XP, Billesbølle CB, Liu Y, Che T, Deshpande I, Jewell M, Fink EA, Kondratov IS, Moroz YS, Irwin JJ, Basbaum AI, Roth BL, Shoichet BK
• Preparing for the next pandemic.
  Science (New York, N.Y.) 2023 Shoichet BK, Craik CS
• Colloidal aggregation confounds cell-based Covid-19 antiviral screens.
  bioRxiv : the preprint server for biology 2023 Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK
• Docking for molecules that bind in a symmetric stack with SymDOCK.
  bioRxiv : the preprint server for biology 2023 Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK
• Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
  Nature communications 2023 Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, …
• Cryo-EM structure of Alzheimer's disease tau filaments with PET ligand MK-6240.
  bioRxiv : the preprint server for biology 2023 Kunach P, Vaquer-Alicea J, Smith MS, Hopewell R, Monistrol J, Moquin L, Therriault J, Tissot C, Rahmouni N, Massarweh G, Soucy JP, Guiot MC, Shoichet BK, Rosa-Neto P, Diamond MI, Shahmoradian SH
• Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase.
  Nature communications 2023 Feng S, Puchades C, Ko J, Wu H, Chen Y, Figueroa EE, Gu S, Han TW, Ho B, Cheng T, Li J, Shoichet B, Jan YN, Cheng Y, Jan LY
• Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.
  Protein science : a publication of the Protein Society 2023 Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons…
• Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.
  Journal of medicinal chemistry 2023 Singh I, Li F, Fink EA, Chau I, Li A, Rodriguez-Hernández A, Glenn I, Zapatero-Belinchón FJ, Rodriguez ML, Devkota K, Deng Z, White K, Wan X, Tolmachova NA, Moroz YS, Kaniskan HÜ, Ott M, García-Sastre…
• Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.
  Cell 2023 Singh I, Seth A, Billesbølle CB, Braz J, Rodriguiz RM, Roy K, Bekele B, Craik V, Huang XP, Boytsov D, Pogorelov VM, Lak P, O'Donnell H, Sandtner W, Irwin JJ, Roth BL, Basbaum AI, Wetsel WC, Manglik A,…
• Synthetic Ionizable Colloidal Drug Aggregates Enable Endosomal Disruption.
  Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2023 Donders EN, Slaughter KV, Dank C, Ganesh AN, Shoichet BK, Lautens M, Shoichet MS
• Modeling the expansion of virtual screening libraries.
  Nature chemical biology 2023 Lyu J, Irwin JJ, Shoichet BK
• Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2.
  Nature microbiology 2023 Yang J, Xiao Y, Lidsky PV, Wu CT, Bonser LR, Peng S, Garcia-Knight MA, Tassetto M, Chung CI, Li X, Nakayama T, Lee IT, Nayak JV, Ghias K, Hargett KL, Shoichet BK, Erle DJ, Jackson PK, Andino R, Shu X
• Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, …
• Ligand recognition and allosteric modulation of the human MRGPRX1 receptor.
  Nature chemical biology 2022 Liu Y, Cao C, Huang XP, Gumpper RH, Rachman MM, Shih SL, Krumm BE, Zhang S, Shoichet BK, Fay JF, Roth BL
• Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor.
  Science (New York, N.Y.) 2022 Fink EA, Xu J, Hübner H, Braz JM, Seemann P, Avet C, Craik V, Weikert D, Schmidt MF, Webb CM, Tolmachova NA, Moroz YS, Huang XP, Kalyanaraman C, Gahbauer S, Chen G, Liu Z, Jacobson MP, Irwin JJ, …
• Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity.
  Nature 2022 Kaplan AL, Confair DN, Kim K, Barros-Álvarez X, Rodriguiz RM, Yang Y, Kweon OS, Che T, McCorvy JD, Kamber DN, Phelan JP, Martins LC, Pogorelov VM, DiBerto JF, Slocum ST, Huang XP, Kumar JM, Robertson …
• Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2.
  bioRxiv : the preprint server for biology 2022 Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko D, Moroz Y, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, …
• Inactive and active state structures template selective tools for the human 5-HT5A receptor.
  Nature structural & molecular biology 2022 Zhang S, Chen H, Zhang C, Yang Y, Popov P, Liu J, Krumm BE, Cao C, Kim K, Xiong Y, Katritch V, Shoichet BK, Jin J, Fay JF, Roth BL
• Drug building blocks and libraries at risk in Ukraine.
  Science (New York, N.Y.) 2022 Kondratov IS, Moroz YS, Irwin JJ, Shoichet BK
• Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor.
  Journal of medicinal chemistry 2022 Levit Kaplan A, Strachan RT, Braz JM, Craik V, Slocum S, Mangano T, Amabo V, O'Donnell H, Lak P, Basbaum AI, Roth BL, Shoichet BK
• Identification of a conserved drug binding pocket in TMEM16 proteins.
  Research square 2022 Cheng Y, Feng S, Puchades C, Ko J, Figueroa E, Chen Y, Wu H, Gu S, Han T, Li J, Ho B, Shoichet B, Jan YN, Jan L
• Publisher Correction: A practical guide to large-scale docking.
  Nature protocols 2022 Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK
• Structures of the σ2 receptor enable docking for bioactive ligand discovery.
  Nature 2021 Alon A, Lyu J, Braz JM, Tummino TA, Craik V, O'Meara MJ, Webb CM, Radchenko DS, Moroz YS, Huang XP, Liu Y, Roth BL, Irwin JJ, Basbaum AI, Shoichet BK, Kruse AC
• Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens.
  Journal of medicinal chemistry 2021 O'Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK
• Structure, function and pharmacology of human itch GPCRs.
  Nature 2021 Cao C, Kang HJ, Singh I, Chen H, Zhang C, Ye W, Hayes BW, Liu J, Gumpper RH, Bender BJ, Slocum ST, Krumm BE, Lansu K, McCorvy JD, Kroeze WK, English JG, DiBerto JF, Olsen RHJ, Huang XP, Zhang S, Liu Y…
• Efficient Exploration of Chemical Space with Docking and Deep Learning.
  Journal of chemical theory and computation 2021 Yang Y, Yao K, Repasky MP, Leswing K, Abel R, Shoichet BK, Jerome SV
• A practical guide to large-scale docking.
  Nature protocols 2021 Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK
• Energy penalties enhance flexible receptor docking in a model cavity.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK
• Ligand Strain Energy in Large Library Docking.
  Journal of chemical information and modeling 2021 Gu S, Smith MS, Yang Y, Irwin JJ, Shoichet BK
• Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens.
  bioRxiv : the preprint server for biology 2021 Oâ Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK
• Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.
  Science (New York, N.Y.) 2021 Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, White KM, Zhang Z, Alon A, Schadt H, O'Donnell HR, Lyu J, Rosales R, McGovern BL, Rathnasinghe R, Jangra S, Schotsaert M, …
• Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
  Science advances 2021 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N,…
• A Crowding Barrier to Protein Inhibition in Colloidal Aggregates.
  Journal of medicinal chemistry 2021 Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK
• Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2.
  bioRxiv : the preprint server for biology 2021 Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, Zhang Z, Alon A, O'Donnell HR, Lyu J, Schadt H, White KM, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz…
• Property-Unmatched Decoys in Docking Benchmarks.
  Journal of chemical information and modeling 2021 Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ
• Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking.
  bioRxiv : the preprint server for biology 2020 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, …
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  Science (New York, N.Y.) 2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor…
• Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor.
  Cell 2020 Kim K, Che T, Panova O, DiBerto JF, Lyu J, Krumm BE, Wacker D, Robertson MJ, Seven AB, Nichols DE, Shoichet BK, Skiniotis G, Roth BL
• Differential Roles of Extracellular Histidine Residues of GPR68 for Proton-Sensing and Allosteric Modulation by Divalent Metal Ions.
  Biochemistry 2020 Huang XP, Kenakin TP, Gu S, Shoichet BK, Roth BL
• The activities of drug inactive ingredients on biological targets.
  Science (New York, N.Y.) 2020 Pottel J, Armstrong D, Zou L, Fekete A, Huang XP, Torosyan H, Bednarczyk D, Whitebread S, Bhhatarai B, Liang G, Jin H, Ghaemi SN, Slocum S, Lukacs KV, Irwin JJ, Berg EL, Giacomini KM, Roth BL, …
• The Global Phosphorylation Landscape of SARS-CoV-2 Infection.
  Cell 2020 Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray…
• Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Zou L, Spanogiannopoulos P, Pieper LM, Chien HC, Cai W, Khuri N, Pottel J, Vora B, Ni Z, Tsakalozou E, Zhang W, Shoichet BK, Giacomini KM, Turnbaugh PJ
• An allosteric modulator binds to a conformational hub in the β2 adrenergic receptor.
  Nature chemical biology 2020 Liu X, Kaindl J, Korczynska M, Stößel A, Dengler D, Stanek M, Hübner H, Clark MJ, Mahoney J, Matt RA, Xu X, Hirata K, Shoichet BK, Sunahara RK, Kobilka BK, Gmeiner P
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, …
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
  bioRxiv : the preprint server for biology 2020 Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, …
• Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.
  Journal of the American Chemical Society 2020 Wan X, Yang T, Cuesta A, Pang X, Balius TE, Irwin JJ, Shoichet BK, Taunton J
• Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP.
  Molecular pharmaceutics 2020 Zou L, Pottel J, Khuri N, Ngo HX, Ni Z, Tsakalozou E, Warren MS, Huang Y, Shoichet BK, Giacomini KM
• Virtual discovery of melatonin receptor ligands to modulate circadian rhythms.
  Nature 2020 Stein RM, Kang HJ, McCorvy JD, Glatfelter GC, Jones AJ, Che T, Slocum S, Huang XP, Savych O, Moroz YS, Stauch B, Johansson LC, Cherezov V, Kenakin T, Irwin JJ, Shoichet BK, Roth BL, Dubocovich ML
• GAIN domain-mediated cleavage is required for activation of G protein-coupled receptor 56 (GPR56) by its natural ligands and a small-molecule agonist.
  The Journal of biological chemistry 2019 Zhu B, Luo R, Jin P, Li T, Oak HC, Giera S, Monk KR, Lak P, Shoichet BK, Piao X
• Protein Stability Effects in Aggregate-Based Enzyme Inhibition.
  Journal of medicinal chemistry 2019 Torosyan H, Shoichet BK
• Triggered Release Enhances the Cytotoxicity of Stable Colloidal Drug Aggregates.
  ACS chemical biology 2019 Donders EN, Ganesh AN, Torosyan H, Lak P, Shoichet BK, Shoichet MS
• Structural identification of a hotspot on CFTR for potentiation.
  Science (New York, N.Y.) 2019 Liu F, Zhang Z, Levit A, Levring J, Touhara KK, Shoichet BK, Chen J
• Colloidal Drug Aggregate Stability in High Serum Conditions and Pharmacokinetic Consequence.
  ACS chemical biology 2019 Ganesh AN, Aman A, Logie J, Barthel BL, Cogan P, Al-Awar R, Koch TH, Shoichet BK, Shoichet MS
• Ultra-large library docking for discovering new chemotypes.
  Nature 2019 Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ
• Far away from the lamppost.
  PLoS biology 2018 Oprea TI, Jan L, Johnson GL, Roth BL, Ma'ayan A, Schürer S, Shoichet BK, Sklar LA, McManus MT
• Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Liu H, Hofmann J, Fish I, Schaake B, Eitel K, Bartuschat A, Kaindl J, Rampp H, Banerjee A, Hübner H, Clark MJ, Vincent SG, Fisher JT, Heinrich MR, Hirata K, Liu X, Sunahara RK, Shoichet BK, Kobilka BK…
• The Recognition of Unrelated Ligands by Identical Proteins.
  ACS chemical biology 2018 Pottel J, Levit A, Korczynska M, Fischer M, Shoichet BK
• The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
  Cell 2018 Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, …
• Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets.
  Journal of medicinal chemistry 2018 Weiss DR, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK
• Colloidal aggregation: from screening nuisance to formulation nuance.
  Nano today 2018 Ganesh AN, Donders EN, Shoichet BK, Shoichet MS
• Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Korczynska M, Clark MJ, Valant C, Xu J, Moo EV, Albold S, Weiss DR, Torosyan H, Huang W, Kruse AC, Lyda BR, May LT, Baltos JA, Sexton PM, Kobilka BK, Christopoulos A, Shoichet BK, Sunahara RK
• Prediction of enzymatic pathways by integrative pathway mapping.
  eLife 2018 Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, …
• Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone.
  Nature 2018 Wang S, Che T, Levit A, Shoichet BK, Wacker D, Roth BL
• Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs.
  Nature chemical biology 2017 McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL
• Structure-Based Design and Discovery of New M2 Receptor Agonists.
  Journal of medicinal chemistry 2017 Fish I, Stößel A, Eitel K, Valant C, Albold S, Huebner H, Möller D, Clark MJ, Sunahara RK, Christopoulos A, Shoichet BK, Gmeiner P
• D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.
  Science (New York, N.Y.) 2017 Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL
• Discovery of new GPCR ligands to illuminate new biology.
  Nature chemical biology 2017 Roth BL, Irwin JJ, Shoichet BK
• Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets.
  eLife 2017 Maciejewski M, Lounkine E, Whitebread S, Farmer P, DuMouchel W, Shoichet BK, Urban L
• Testing inhomogeneous solvation theory in structure-based ligand discovery.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK
• Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations.
  Molecular pharmaceutics 2017 Ganesh AN, Logie J, McLaughlin CK, Barthel BL, Koch TH, Shoichet BK, Shoichet MS
• A New Spin on Antibody-Drug Conjugates: Trastuzumab-Fulvestrant Colloidal Drug Aggregates Target HER2-Positive Cells.
  ACS applied materials & interfaces 2017 Ganesh AN, McLaughlin CK, Duan D, Shoichet BK, Shoichet MS
• In silico design of novel probes for the atypical opioid receptor MRGPRX2.
  Nature chemical biology 2017 Lansu K, Karpiak J, Liu J, Huang XP, McCorvy JD, Kroeze WK, Che T, Nagase H, Carroll FI, Jin J, Shoichet BK, Roth BL
• Crystal Structure of an LSD-Bound Human Serotonin Receptor.
  Cell 2017 Wacker D, Wang S, McCorvy JD, Betz RM, Venkatakrishnan AJ, Levit A, Lansu K, Schools ZL, Che T, Nichols DE, Shoichet BK, Dror RO, Roth BL
• Internal Structure and Preferential Protein Binding of Colloidal Aggregates.
  ACS chemical biology 2016 Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK
• Design, Synthesis, and Biological Evaluation of Novel Tetrahydroprotoberberine Derivatives (THPBs) as Selective α1A-Adrenoceptor Antagonists.
  Journal of medicinal chemistry 2016 Guo D, Li J, Lin H, Zhou Y, Chen Y, Zhao F, Sun H, Zhang D, Li H, Shoichet BK, Shan L, Zhang W, Xie X, Jiang H, Liu H
• A Molecular Basis for Innovation in Drug Excipients.
  Clinical pharmacology and therapeutics 2016 Irwin JJ, Pottel J, Zou L, Wen H, Zuk S, Zhang X, Sterling T, Shoichet BK, Lionberger R, Giacomini KM
• Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.
  Journal of the American Chemical Society 2016 Lee H, Fischer M, Shoichet BK, Liu SY
• Structure-based discovery of opioid analgesics with reduced side effects.
  Nature 2016 Manglik A, Lin H, Aryal DK, McCorvy JD, Dengler D, Corder G, Levit A, Kling RC, Bernat V, Hübner H, Huang XP, Sassano MF, Giguère PM, Löber S, Scherrer G, Kobilka BK, Gmeiner P, Roth BL, Shoichet BK
• Identification of Novel Smoothened Ligands Using Structure-Based Docking.
  PloS one 2016 Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S
• Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.
  PloS one 2016 O'Meara MJ, Ballouz S, Shoichet BK, Gillis J
• Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward.
  Journal of medicinal chemistry 2016 Shoichet BK, Walters WP, Jiang H, Bajorath J
• Docking Screens for Novel Ligands Conferring New Biology.
  Journal of medicinal chemistry 2016 Irwin JJ, Shoichet BK
• In Vitro and In Vivo Characterization of the Alkaloid Nuciferine.
  PloS one 2016 Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, …
• Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.
  ACS chemical biology 2016 McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS
• Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.
  Journal of medicinal chemistry 2015 Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG
• Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65.
  Nature 2015 Huang XP, Karpiak J, Kroeze WK, Zhu H, Chen X, Moy SS, Saddoris KA, Nikolova VD, Farrell MS, Wang S, Mangano TJ, Deshpande DA, Jiang A, Penn RB, Jin J, Koller BH, Kenakin T, Shoichet BK, Roth BL
• Corrigendum: The promise and peril of chemical probes.
  Nature chemical biology 2015 Arrowsmith CH, Audia JE, Austin C, Baell J, Bennett J, Blagg J, Bountra C, Brennan PE, Brown PJ, Bunnage ME, Buser-Doepner C, Campbell RM, Carter AJ, Cohen P, Copeland RA, Cravatt B, Dahlin JL, Dhanak…
• Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.
  Journal of medicinal chemistry 2015 Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA
• The Recognition of Identical Ligands by Unrelated Proteins.
  ACS chemical biology 2015 Barelier S, Sterling T, O'Meara MJ, Shoichet BK
• Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.
  ACS chemical biology 2015 Pimentel-Elardo SM, Sørensen D, Ho L, Ziko M, Bueler SA, Lu S, Tao J, Moser A, Lee R, Agard D, Fairn G, Rubinstein JL, Shoichet BK, Nodwell JR
• Prediction and validation of enzyme and transporter off-targets for metformin.
  Journal of pharmacokinetics and pharmacodynamics 2015 Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM
• An Aggregation Advisor for Ligand Discovery.
  Journal of medicinal chemistry 2015 Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK
• Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents.
  ACS chemical biology 2015 Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL
• The promise and peril of chemical probes.
  Nature chemical biology 2015 Arrowsmith CH, Audia JE, Austin C, Baell J, Bennett J, Blagg J, Bountra C, Brennan PE, Brown PJ, Bunnage ME, Buser-Doepner C, Campbell RM, Carter AJ, Cohen P, Copeland RA, Cravatt B, Dahlin JL, Dhanak…
• One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.
  Chembiochem : a European journal of chemical biology 2015 Fischer M, Shoichet BK, Fraser JS
• Homologous ligands accommodated by discrete conformations of a buried cavity.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK
• Erratum: Covalent docking of large libraries for the discovery of chemical probes.
  Nature chemical biology 2015 London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J
• Colloidal aggregation and the in vitro activity of traditional Chinese medicines.
  ACS chemical biology 2015 Duan D, Doak AK, Nedyalkova L, Shoichet BK
• Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.
  Biochemistry 2015 London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK
• Covalent docking of large libraries for the discovery of chemical probes.
  Nature chemical biology 2014 London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J
• Actin is required for IFT regulation in Chlamydomonas reinhardtii.
  Current biology : CB 2014 Avasthi P, Onishi M, Karpiak J, Yamamoto R, Mackinder L, Jonikas MC, Sale WS, Shoichet B, Pringle JR, Marshall WF
• 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.
  Biochemistry 2014 Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM
• Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative.
  Journal of medicinal chemistry 2014 Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP
• Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
  Nature chemistry 2014 Fischer M, Coleman RG, Fraser JS, Shoichet BK
• Increasing chemical space coverage by combining empirical and computational fragment screens.
  ACS chemical biology 2014 Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G
• Prediction of substrates for glutathione transferases by covalent docking.
  Journal of chemical information and modeling 2014 Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A
• Substrate deconstruction and the nonadditivity of enzyme recognition.
  Journal of the American Chemical Society 2014 Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK
• Large-scale identification and analysis of suppressive drug interactions.
  Chemistry & biology 2014 Cokol M, Weinstein ZB, Yilancioglu K, Tasan M, Doak A, Cansever D, Mutlu B, Li S, Rodriguez-Esteban R, Akhmedov M, Guvenek A, Cokol M, Cetiner S, Giaever G, Iossifov I, Nislow C, Shoichet B, Roth FP
• Drug discovery: follow your lead.
  Nature chemical biology 2014 Shoichet BK
• Colloidal drug formulations can explain "bell-shaped" concentration-response curves.
  ACS chemical biology 2014 Owen SC, Doak AK, Ganesh AN, Nedyalkova L, McLaughlin CK, Shoichet BK, Shoichet MS
• In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding.
  PLoS biology 2013 Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K
• Ligand pose and orientational sampling in molecular docking.
  PloS one 2013 Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK
• Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.
  Biochemistry 2013 Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM
• Structure-guided discovery of new deaminase enzymes.
  Journal of the American Chemical Society 2013 Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM
• Blind prediction of charged ligand binding affinities in a model binding site.
  Journal of molecular biology 2013 Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA
• Muscarinic receptors as model targets and antitargets for structure-based ligand discovery.
  Molecular pharmacology 2013 Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK
• Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.
  PloS one 2013 Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK
• Structure-based discovery of antagonists of nuclear receptor LRH-1.
  The Journal of biological chemistry 2013 Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ
• Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor.
  ACS chemical biology 2013 Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK
• The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition.
  Journal of medicinal chemistry 2013 Merski M, Shoichet BK
• Colloidal aggregation causes inhibition of G protein-coupled receptors.
  Journal of medicinal chemistry 2013 Sassano MF, Doak AK, Roth BL, Shoichet BK
• Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4).
  Biochemical pharmacology 2013 Cameron RT, Coleman RG, Day JP, Yalla KC, Houslay MD, Adams DR, Shoichet BK, Baillie GS
• A pharmacological organization of G protein-coupled receptors.
  Nature methods 2013 Lin H, Sassano MF, Roth BL, Shoichet BK
• Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.
  Journal of the American Chemical Society 2013 Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM
• Drug discovery: nature's pieces.
  Nature chemistry 2013 Shoichet BK
• Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily.
  Biochemistry 2012 Ornelas A, Korczynska M, Ragumani S, Kumaran D, Narindoshvili T, Shoichet BK, Swaminathan S, Raushel FM
• Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F
• Engineering a model protein cavity to catalyze the Kemp elimination.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Merski M, Shoichet BK
• Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
  Journal of medicinal chemistry 2012 Mysinger MM, Carchia M, Irwin JJ, Shoichet BK
• Identifying mechanism-of-action targets for drugs and probes.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Gregori-Puigjané E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK
• Large-scale prediction and testing of drug activity on side-effect targets.
  Nature 2012 Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L
• Colloidal aggregation affects the efficacy of anticancer drugs in cell culture.
  ACS chemical biology 2012 Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK
• Structure-based drug screening for G-protein-coupled receptors.
  Trends in pharmacological sciences 2012 Shoichet BK, Kobilka BK
• Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Mysinger MM, Weiss DR, Ziarek JJ, Gravel S, Doak AK, Karpiak J, Heveker N, Shoichet BK, Volkman BF
• A chemical screen identifies class a g-protein coupled receptors as regulators of cilia.
  ACS chemical biology 2012 Avasthi P, Marley A, Lin H, Gregori-Puigjane E, Shoichet BK, von Zastrow M, Marshall WF
• Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.
  Biochemistry 2012 Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM
• Chemical informatics and target identification in a zebrafish phenotypic screen.
  Nature chemical biology 2011 Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK
• Statistical potential for modeling and ranking of protein-ligand interactions.
  Journal of chemical information and modeling 2011 Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A
• The Enzyme Function Initiative.
  Biochemistry 2011 Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV
• Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
  Nature chemical biology 2011 Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK
• Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A
• A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets.
  The Journal of biological chemistry 2011 Poncet-Montange G, St Martin SJ, Bogatova OV, Prusiner SB, Shoichet BK, Ghaemmaghami S
• Enzymatic deamination of the epigenetic base N-6-methyladenine.
  Journal of the American Chemical Society 2011 Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM
• The chemical basis of pharmacology.
  Biochemistry 2010 Keiser MJ, Irwin JJ, Shoichet BK
• Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as β-lactamase inhibitors.
  Journal of medicinal chemistry 2010 Eidam O, Romagnoli C, Caselli E, Babaoglu K, Pohlhaus DT, Karpiak J, Bonnet R, Shoichet BK, Prati F
• The presynaptic component of the serotonergic system is required for clozapine's efficacy.
  Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2010 Yadav PN, Abbas AI, Farrell MS, Setola V, Sciaky N, Huang XP, Kroeze WK, Crawford LK, Piel DA, Keiser MJ, Irwin JJ, Shoichet BK, Deneris ES, Gingrich J, Beck SG, Roth BL
• Rapid context-dependent ligand desolvation in molecular docking.
  Journal of chemical information and modeling 2010 Mysinger MM, Shoichet BK
• Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.
  Journal of medicinal chemistry 2010 Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK
• Colloid formation by drugs in simulated intestinal fluid.
  Journal of medicinal chemistry 2010 Doak AK, Wille H, Prusiner SB, Shoichet BK
• Structure-based discovery of A2A adenosine receptor ligands.
  Journal of medicinal chemistry 2010 Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA
• Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.
  Bioorganic & medicinal chemistry letters 2010 Tondi D, Calò S, Shoichet BK, Costi MP
• Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.
  Journal of medicinal chemistry 2010 DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD
• The hunt for 8-oxoguanine deaminase.
  Journal of the American Chemical Society 2010 Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM
• Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
  Biochemistry 2010 Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM
• Rapid behavior-based identification of neuroactive small molecules in the zebrafish.
  Nature chemical biology 2010 Kokel D, Bryan J, Laggner C, White R, Cheung CY, Mateus R, Healey D, Kim S, Werdich AA, Haggarty SJ, Macrae CA, Shoichet B, Peterson RT
• Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB.
  Journal of medicinal chemistry 2010 Mott BT, Ferreira RS, Simeonov A, Jadhav A, Ang KK, Leister W, Shen M, Silveira JT, Doyle PS, Arkin MR, McKerrow JH, Inglese J, Austin CP, Thomas CJ, Shoichet BK, Maloney DJ
• Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease.
  Journal of medicinal chemistry 2010 Jadhav A, Ferreira RS, Klumpp C, Mott BT, Austin CP, Inglese J, Thomas CJ, Maloney DJ, Shoichet BK, Simeonov A
• Structural bases for stability-function tradeoffs in antibiotic resistance.
  Journal of molecular biology 2009 Thomas VL, McReynolds AC, Shoichet BK
• Molecular docking screens using comparative models of proteins.
  Journal of chemical information and modeling 2009 Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A
• Predicting new molecular targets for known drugs.
  Nature 2009 Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KL, Edwards DD, Shoichet BK, Roth BL
• Crystal structures of penicillin-binding protein 6 from Escherichia coli.
  Journal of the American Chemical Society 2009 Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK
• Automated docking screens: a feasibility study.
  Journal of medicinal chemistry 2009 Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y
• Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
  Journal of molecular biology 2009 Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK
• Docking and chemoinformatic screens for new ligands and targets.
  Current opinion in biotechnology 2009 Kolb P, Ferreira RS, Irwin JJ, Shoichet BK
• Divergent modes of enzyme inhibition in a homologous structure-activity series.
  Journal of medicinal chemistry 2009 Ferreira RS, Bryant C, Ang KK, McKerrow JH, Shoichet BK, Renslo AR
• Quantifying biogenic bias in screening libraries.
  Nature chemical biology 2009 Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK
• Docking for fragment inhibitors of AmpC beta-lactamase.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK
• Promiscuous aggregate-based inhibitors promote enzyme unfolding.
  Journal of medicinal chemistry 2009 Coan KE, Maltby DA, Burlingame AL, Shoichet BK
• Structure-based discovery of beta2-adrenergic receptor ligands.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK
• Molecular docking and ligand specificity in fragment-based inhibitor discovery.
  Nature chemical biology 2009 Chen Y, Shoichet BK
• Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily.
  Biochemistry 2009 Xiang DF, Kolb P, Fedorov AA, Meier MM, Fedorov LV, Nguyen TT, Sterner R, Almo SC, Shoichet BK, Raushel FM
• Re-examining the role of Lys67 in class C beta-lactamase catalysis.
  Protein science : a publication of the Protein Society 2009 Chen Y, McReynolds A, Shoichet BK
• Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase.
  Journal of molecular biology 2008 Marciano DC, Pennington JM, Wang X, Wang J, Chen Y, Thomas VL, Shoichet BK, Palzkill T
• Exploiting ordered waters in molecular docking.
  Journal of medicinal chemistry 2008 Huang N, Shoichet BK
• Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors.
  Journal of the American Chemical Society 2008 Coan KE, Shoichet BK
• Quantifying the relationships among drug classes.
  Journal of chemical information and modeling 2008 Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK
• Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
  Journal of medicinal chemistry 2008 Babaoglu K, Simeonov A, Irwin JJ, Nelson ME, Feng B, Thomas CJ, Cancian L, Costi MP, Maltby DA, Jadhav A, Inglese J, Austin CP, Shoichet BK
• Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
  Journal of molecular biology 2008 Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK
• Small-molecule aggregates inhibit amyloid polymerization.
  Nature chemical biology 2008 Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK
• Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors.
  Bioorganic & medicinal chemistry 2007 Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F
• Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy.
  Journal of medicinal chemistry 2007 Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G, Shoichet BK, Costi MP
• Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases.
  Journal of molecular biology 2007 Delmas J, Chen Y, Prati F, Robin F, Shoichet BK, Bonnet R
• No free energy lunch.
  Nature biotechnology 2007 Shoichet BK
• O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site.
  Journal of the American Chemical Society 2007 Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF
• Structure-based activity prediction for an enzyme of unknown function.
  Nature 2007 Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM
• Predicting absolute ligand binding free energies to a simple model site.
  Journal of molecular biology 2007 Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA
• Stability for function trade-offs in the enolase superfamily "catalytic module".
  Biochemistry 2007 Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC
• A high-throughput screen for aggregation-based inhibition in a large compound library.
  Journal of medicinal chemistry 2007 Feng BY, Simeonov A, Jadhav A, Babaoglu K, Inglese J, Shoichet BK, Austin CP
• The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution.
  Journal of the American Chemical Society 2007 Chen Y, Bonnet R, Shoichet BK
• An interview with Brian Shoichet, Ph.D. Professor, Department of Pharmaceutical Chemistry, University of California, San Francisco.
  Assay and drug development technologies 2007 Shoichet B
• Relating protein pharmacology by ligand chemistry.
  Nature biotechnology 2007 Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK
• Stability and equilibria of promiscuous aggregates in high protein milieus.
  Molecular bioSystems 2007 Coan KE, Shoichet BK
• Interpreting steep dose-response curves in early inhibitor discovery.
  Journal of medicinal chemistry 2006 Shoichet BK
• Predicting substrates by docking high-energy intermediates to enzyme structures.
  Journal of the American Chemical Society 2006 Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK
• Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library.
  Journal of the American Chemical Society 2006 Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM
• Benchmarking sets for molecular docking.
  Journal of medicinal chemistry 2006 Huang N, Shoichet BK, Irwin JJ
• Deconstructing fragment-based inhibitor discovery.
  Nature chemical biology 2006 Babaoglu K, Shoichet BK
• Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.
  Journal of medicinal chemistry 2006 Leach AR, Shoichet BK, Peishoff CE
• Screening in a spirit haunted world.
  Drug discovery today 2006 Shoichet BK
• Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures.
  Journal of medicinal chemistry 2006 Feng BY, Shoichet BK
• The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.
  Journal of the American Chemical Society 2006 Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK
• Probing molecular docking in a charged model binding site.
  Journal of molecular biology 2006 Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK
• A detergent-based assay for the detection of promiscuous inhibitors.
  Nature protocols 2006 Feng BY, Shoichet BK
• Virtual screening against metalloenzymes for inhibitors and substrates.
  Biochemistry 2005 Irwin JJ, Raushel FM, Shoichet BK
• Here be dragons: docking and screening in an uncharted region of chemical space.
  Journal of biomolecular screening 2005 Brenk R, Irwin JJ, Shoichet BK
• Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase.
  Biochemistry 2005 Thomas VL, Golemi-Kotra D, Kim C, Vakulenko SB, Mobashery S, Shoichet BK
• High-throughput assays for promiscuous inhibitors.
  Nature chemical biology 2005 Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK
• Decoys for docking.
  Journal of medicinal chemistry 2005 Graves AP, Brenk R, Shoichet BK
• Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability.
  Journal of molecular biology 2005 Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R
• Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases.
  Journal of the American Chemical Society 2005 Chen Y, Shoichet B, Bonnet R
• Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture.
  Journal of the American Chemical Society 2005 Tondi D, Morandi F, Bonnet R, Costi MP, Shoichet BK
• Hierarchical docking of databases of multiple ligand conformations.
  Current topics in medicinal chemistry 2005 Lorber DM, Shoichet BK
• ZINC--a free database of commercially available compounds for virtual screening.
  Journal of chemical information and modeling 2005 Irwin JJ, Shoichet BK
• Virtual screening of chemical libraries.
  Nature 2004 Shoichet BK
• Soft docking and multiple receptor conformations in virtual screening.
  Journal of medicinal chemistry 2004 Ferrari AM, Wei BQ, Costantino L, Shoichet BK
• Testing a flexible-receptor docking algorithm in a model binding site.
  Journal of molecular biology 2004 Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK
• Allosteric inhibition through core disruption.
  Journal of molecular biology 2004 Horn JR, Shoichet BK
• Thermodynamic cycle analysis and inhibitor design against beta-lactamase.
  Biochemistry 2003 Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK
• Identification and prediction of promiscuous aggregating inhibitors among known drugs.
  Journal of medicinal chemistry 2003 Seidler J, McGovern SL, Doman TN, Shoichet BK
• A specific mechanism of nonspecific inhibition.
  Journal of medicinal chemistry 2003 McGovern SL, Helfand BT, Feng B, Shoichet BK
• Structural aspects for evolution of beta-lactamases from penicillin-binding proteins.
  Journal of the American Chemical Society 2003 Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S
• Recognition and resistance in TEM beta-lactamase.
  Biochemistry 2003 Wang X, Minasov G, Blázquez J, Caselli E, Prati F, Shoichet BK
• Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.
  Journal of medicinal chemistry 2003 McGovern SL, Shoichet BK
• Kinase inhibitors: not just for kinases anymore.
  Journal of medicinal chemistry 2003 McGovern SL, Shoichet BK
• Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough.
  The Journal of biological chemistry 2003 Soelaiman S, Wei BQ, Bergson P, Lee YS, Shen Y, Mrksich M, Shoichet BK, Tang WJ
• A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase.
  The Journal of biological chemistry 2003 Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS
• Nanomolar inhibitors of AmpC beta-lactamase.
  Journal of the American Chemical Society 2003 Morandi F, Caselli E, Morandi S, Focia PJ, Blázquez J, Shoichet BK, Prati F
• A model binding site for testing scoring functions in molecular docking.
  Journal of molecular biology 2002 Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK
• Structural bases of stability-function tradeoffs in enzymes.
  Journal of molecular biology 2002 Beadle BM, Shoichet BK
• Lead discovery using molecular docking.
  Current opinion in chemical biology 2002 Shoichet BK, McGovern SL, Wei B, Irwin JJ
• Structure-based approach for binding site identification on AmpC beta-lactamase.
  Journal of medicinal chemistry 2002 Powers RA, Shoichet BK
• Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.
  Structure (London, England : 1993) 2002 Powers RA, Morandi F, Shoichet BK
• Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.
  Journal of molecular biology 2002 Wang X, Minasov G, Shoichet BK
• Protein-protein docking with multiple residue conformations and residue substitutions.
  Protein science : a publication of the Protein Society 2002 Lorber DM, Udo MK, Shoichet BK
• Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.
  Journal of medicinal chemistry 2002 Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK
• An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation.
  Journal of the American Chemical Society 2002 Minasov G, Wang X, Shoichet BK
• A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening.
  Journal of medicinal chemistry 2002 McGovern SL, Caselli E, Grigorieff N, Shoichet BK
• Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.
  Proteins 2002 Wang X, Minasov G, Shoichet BK
• Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
  Structure (London, England : 1993) 2002 Beadle BM, Trehan I, Focia PJ, Shoichet BK
• Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.
  Biochemistry 2001 Trehan I, Beadle BM, Shoichet BK
• Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation.
  Protein science : a publication of the Protein Society 2001 Beadle BM, Nicholas RA, Shoichet BK
• Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase.
  Chemistry & biology 2001 Tondi D, Powers RA, Caselli E, Negri MC, Blázquez J, Costi MP, Shoichet BK
• Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation.
  Proteins 2001 Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK
• Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.
  Chemistry & biology 2001 Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK
• The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
  Protein science : a publication of the Protein Society 1999 Powers RA, Blázquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK
• Functional analyses of AmpC beta-lactamase through differential stability.
  Protein science : a publication of the Protein Society 1999 Beadle BM, McGovern SL, Patera A, Shoichet BK
• Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase.
  Chemistry & biology 1999 Tondi D, Slomczynska U, Costi MP, Watterson DM, Ghelli S, Shoichet BK
• Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme.
  Biochemistry 1999 Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK
• Structure-based design of inhibitors specific for bacterial thymidylate synthase.
  Biochemistry 1999 Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP
• Ligand solvation in molecular docking.
  Proteins 1999 Shoichet BK, Leach AR, Kuntz ID
• 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.
  Biochemistry 1998 Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ
• Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase.
  Journal of medicinal chemistry 1998 Weston GS, Blázquez J, Baquero F, Shoichet BK
• An extended-spectrum AmpC-type beta-lactamase obtained by in vitro antibiotic selection.
  FEMS microbiology letters 1998 Morosini MI, Negri MC, Shoichet B, Baquero MR, Baquero F, Blázquez J
• Flexible ligand docking using conformational ensembles.
  Protein science : a publication of the Protein Society 1998 Lorber DM, Shoichet BK
• Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.
  Nature structural biology 1996 Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN
• Predicting the structure of protein complexes: a step in the right direction.
  Chemistry & biology 1996 Shoichet BK, Kuntz ID
• Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive.
  Protein engineering 1995 Zhang XJ, Baase WA, Shoichet BK, Wilson KP, Matthews BW
• A relationship between protein stability and protein function.
  Proceedings of the National Academy of Sciences of the United States of America 1995 Shoichet BK, Baase WA, Kuroki R, Matthews BW
• Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion.
  Biochemistry 1994 Schellenberger U, Balaram P, Francis VS, Shoichet BK, Santi DV
• Matching chemistry and shape in molecular docking.
  Protein engineering 1993 Shoichet BK, Kuntz ID
• Structure-based discovery of inhibitors of thymidylate synthase.
  Science (New York, N.Y.) 1993 Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM
• Protein docking and complementarity.
  Journal of molecular biology 1991 Shoichet BK, Kuntz ID
• Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis.
  Protein engineering 1989 Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P