University of California San Francisco

brian-shoichet
Brian Shoichet, PhD

Professor, Pharmaceutical Chemistry

Link to Pharmacy Profile/Bio

Address

1700 4th Street, #508D
San Francisco, CA 94158
United States

Email: [email protected]
Phone: 415-514-4126
Fax: 415-514-4260

Education

Institution Degree Dept or School End Date
University of California, San Francisco Ph.D. Graduate Division (Pharmaceutical Chemistry) 1991

Awards & Honors

Award Conferred By Date
Society for Biomolecular Sciences Accomplishment Award 2011
Topliss Lectureship University of Michigan 2011
Abbott Lectureship Yale University 2009
Swiss Universities 3e Cycle en Chimie (Lausanne, Bern, Friborg, Geneva) 2008
Novartis Chemistry Lecturer (Cambridge, Basel, Vienna, Horsham, Tsukuba, Emeryville) 2006/2007
Astra Lectureship University of Ottawa 2004
Dean’s Award for Teaching Excellence Northwestern University 2001
CAREER Award National Science Foundation 1998/2003
Career Development Award PhRMA Foundation 1997/1999
Damon Runyon-Walter Winchell Cancer Research Fellow 1993/1996

Grants and Funding

  • A Web-Based Automatic Virtual Screening System | NIH | 2004-08-01 - 2025-04-30 | Role: Principal Investigator
  • Degenerative and Dementing Diseases of Aging | NIH | 1981-01-01 - 2025-03-31 | Role: Co-Investigator
  • Illuminating the Druggable GPCR-ome | NIH | 2017-09-15 - 2023-08-31 | Role: Co-Principal Investigator
  • Development and Testing of New Computational Methods for Ligand Discovery and Mechanism | NIH | 2017-06-01 - 2022-05-31 | Role: Principal Investigator
  • Molecular Details of Psychoactive Drug Actions | NIH | 2017-03-06 - 2021-12-31 | Role: Co-Principal Investigator
  • A Specific Mechanism for non-specific inhibition | NIH | 1992-08-01 - 2019-05-31 | Role: Principal Investigator
  • Design and Experimental Testing of New Docking Methods | NIH | 1999-08-01 - 2018-11-30 | Role: Principal Investigator
  • Scalable technologies for illuminating the druggable GPCR-ome | NIH | 2014-08-01 - 2018-04-30 | Role: Co-Principal Investigator
  • Bio-Organic Biomedical Mass Spectrometry Resource | NIH | 1982-03-01 - 2015-05-31 | Role: Co-Investigator
  • Structure, Function and Inhibition of Beta-Lactamases | NIH | 2001-08-01 - 2015-02-28 | Role: Principal Investigator
  • Resource for Biocomputing, Visualization, and Informatics | NIH/NCRR | 1976-06-01 - 2012-09-14 | Role: Co-Investigator
  • Promiscuous and Specific Inhibitors of Cruzain | NIH | 2007-09-01 - 2008-08-31 | Role: Principal Investigator

Publications

MOST RECENT PUBLICATIONS FROM A TOTAL OF 296
  1. Re-examining the role of Lys67 in class C beta-lactamase catalysis.
    Chen Y, McReynolds A, Shoichet BK| | PubMed
  2. Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase.
    Marciano DC, Pennington JM, Wang X, Wang J, Chen Y, Thomas VL, Shoichet BK, Palzkill T| | PubMed
  3. Exploiting ordered waters in molecular docking.
    Huang N, Shoichet BK| | PubMed
  4. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors.
    Coan KE, Shoichet BK| | PubMed
  5. Quantifying the relationships among drug classes.
    Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK| | PubMed
  6. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
    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| | PubMed
  7. Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
    Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK| | PubMed
  8. Small-molecule aggregates inhibit amyloid polymerization.
    Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK| | PubMed
  9. Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors.
    Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F| | PubMed
  10. Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy.
    Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G, Shoichet BK, Costi MP| | PubMed
296
View all 296 Publications
MOST RECENT PUBLICATIONS FROM A TOTAL OF 296
  1. A Database for Large-Scale Docking and Experimental Results.
    Hall BW, Tummino TA, Tang K, Mailhot O, Castanon M, Irwin JJ, Shoichet BK| | PubMed
  2. Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy.
    Detomasi TC, Degotte G, Huang S, Suryawanshi RK, Diallo A, Lizzadro L, Zaptero-Belinchón FJ, Taha TY, Li J, Richards AL, Hantz ER, Alam Z, Montano M, McCavitt-Malvido M, Gumpena R, Partridge JR, Correy GJ, Matsui Y, Charvat AF, Glenn IS, Rosecrans J, Revalde JL, Anderson D, Hultquist JF, Arkin MR, Neitz RJ, Swaney DL, Krogan NJ, Shoichet BK, Verba KA, Ott M, Renslo AR, Craik CS| | PubMed
  3. Characterization of quinazolinone calcilytic therapy for autosomal dominant hypocalcemia type 1 (ADH1).
    Hannan FM, Kooblall KG, Stevenson M, Elajnaf T, Liu F, Lines KE, Meng X, Stewart M, Wells S, Nemeth EF, Shoichet BK, Kneissel M, Gasser JA, Thakker RV| | PubMed
  4. Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects.
    Tummino TA, Iliopoulos-Tsoutsouvas C, Braz JM, O'Brien ES, Stein RM, Craik V, Tran NK, Ganapathy S, Liu F, Shiimura Y, Tong F, Ho TC, Radchenko DS, Moroz YS, Rosado SR, Bhardwaj K, Benitez J, Liu Y, Kandasamy H, Normand C, Semache M, Sabbagh L, Glenn I, Irwin JJ, Kumar KK, Makriyannis A, Basbaum AI, Shoichet BK| | PubMed
  5. A database for large-scale docking and experimental results.
    Hall BW, Tummino TA, Tang K, Irwin JJ, Shoichet BK| | PubMed
  6. A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils.
    Smith MS, DeGrado WF, Grabe M, Shoichet BK| | PubMed
  7. Docking 14 million virtual isoquinuclidines against the mu and kappa opioid receptors reveals dual antagonists-inverse agonists with reduced withdrawal effects.
    Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbølle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK| | PubMed
  8. The impact of library size and scale of testing on virtual screening.
    Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK| | PubMed
  9. Thoughts for the future.
    Alkhalaf LM, Arrowsmith C, Balskus EP, Bergamini G, Bhandari R, Chang CJ, Chen P, Chen X, Ciulli A, Cricco JA, Davis BG, Delbianco M, Dudareva N, Dueber E, Ferguson F, de Giuseppe PO, Hamachi I, Hammond MC, Hatzios SK, Do Heo W, Janet JP, Kamat SS, Knapp S, Krishnan Y, Lang K, Laraia L, Leveson-Gower RB, Li XD, Liu DR, Liu MF, London N, Mahanta N, Mayor-Ruiz C, Muir T, Murakami MT, Rhee HW, Robers M, Satz A, Schulman BA, Shen B, Shoichet B, Strauss E, Suzuki T, Tiwary P, Waldmann H, Ward TR, Weeks A, Weerapana E, Winter G| | PubMed
  10. High-affinity agonists reveal recognition motifs for the MRGPRD GPCR.
    Wang C, Liu Y, Lanier M, Yeager A, Singh I, Gumpper RH, Krumm BE, DeLeon C, Zhang S, Boehm M, Pittner R, Baron A, Dvorak L, Bacon C, Shoichet BK, Martinborough E, Fay JF, Cao C, Roth BL| | PubMed
  11. Cryo-EM structure of Alzheimer's disease tau filaments with PET ligand MK-6240.
    Kunach P, Vaquer-Alicea J, Smith MS, Monistrol J, Hopewell R, Moquin L, Therriault J, Tissot C, Rahmouni N, Massarweh G, Soucy JP, Guiot MC, Shoichet BK, Rosa-Neto P, Diamond MI, Shahmoradian SH| | PubMed
  12. Large library docking identifies positive allosteric modulators of the calcium-sensing receptor.
    Liu F, Wu CG, Tu CL, Glenn I, Meyerowitz J, Kaplan AL, Lyu J, Cheng Z, Tarkhanova OO, Moroz YS, Irwin JJ, Chang W, Shoichet BK, Skiniotis G| | PubMed
  13. Identifying Artifacts from Large Library Docking.
    Wu Y, Liu F, Glenn I, Fonseca-Valencia K, Paris L, Xiong Y, Jerome SV, Brooks CL, Shoichet BK| | PubMed
  14. The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2.
    Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Zapatero-Belinchón FJ, McCavittMalvido M, Doruk YU, Stevens MGV, Diolaiti ME, Jogalekar MP, Richards AL, Montano M, Rosecrans J, Matthay M, Togo T, Gonciarz RL, Gopalkrishnan S, Neitz RJ, Krogan NJ, Swaney DL, Shoichet BK, Ott M, Renslo AR, Ashworth A, Fraser JS| | PubMed
  15. Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning.
    Correy GJ, Rachman M, Togo T, Gahbauer S, Doruk YU, Stevens M, Jaishankar P, Kelley B, Goldman B, Schmidt M, Kramer T, Ashworth A, Riley P, Shoichet BK, Renslo AR, Walters WP, Fraser JS| | PubMed
  16. Ionizable Drugs Enable Intracellular Delivery of Co-Formulated siRNA.
    Slaughter KV, Donders EN, Jones MS, Sabbah SG, Elliott MJ, Shoichet BK, Cescon DW, Shoichet MS| | PubMed
  17. Identifying Artifacts from Large Library Docking.
    Wu Y, Liu F, Glenn I, Fonseca-Valencia K, Paris L, Xiong Y, Jerome SV, Brooks CL, Shoichet BK| | PubMed
  18. The impact of Library Size and Scale of Testing on Virtual Screening.
    Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK| | PubMed
  19. AlphaFold2 structures guide prospective ligand discovery.
    Lyu J, Kapolka N, Gumpper R, Alon A, Wang L, Jain MK, Barros-Álvarez X, Sakamoto K, Kim Y, DiBerto J, Kim K, Glenn IS, Tummino TA, Huang S, Irwin JJ, Tarkhanova OO, Moroz Y, Skiniotis G, Kruse AC, Shoichet BK, Roth BL| | PubMed
  20. Colloidal Aggregation Confounds Cell-Based Covid-19 Antiviral Screens.
    Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK| | PubMed
  21. Structure-based discovery of CFTR potentiators and inhibitors.
    Liu F, Kaplan AL, Levring J, Einsiedel J, Tiedt S, Distler K, Omattage NS, Kondratov IS, Moroz YS, Pietz HL, Irwin JJ, Gmeiner P, Shoichet BK, Chen J| | PubMed
  22. Profiling the proximal proteome of the activated μ-opioid receptor.
    Polacco BJ, Lobingier BT, Blythe EE, Abreu N, Khare P, Howard MK, Gonzalez-Hernandez AJ, Xu J, Li Q, Novy B, Naing ZZC, Shoichet BK, Coyote-Maestas W, Levitz J, Krogan NJ, Von Zastrow M, Hüttenhain R| | PubMed
  23. Discovery of Protease-Activated Receptor 4 (PAR4)-Tethered Ligand Antagonists Using Ultralarge Virtual Screening.
    Smith ST, Cassada JB, Von Bredow L, Erreger K, Webb EM, Trombley TA, Kalbfleisch JJ, Bender BJ, Zagol-Ikapitte I, Kramlinger VM, Bouchard JL, Mitchell SG, Tretbar M, Shoichet BK, Lindsley CW, Meiler J, Hamm HE| | PubMed
  24. AlphaFold2 structures template ligand discovery.
    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, Roth BL| | PubMed
  25. Structure-based discovery of CFTR potentiators and inhibitors.
    Liu F, Kaplan AL, Levring J, Einsiedel J, Tiedt S, Distler K, Omattage NS, Kondratov IS, Moroz YS, Pietz HL, Irwin JJ, Gmeiner P, Shoichet BK, Chen J| | PubMed
  26. Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor.
    Liu F, Wu CG, Tu CL, Glenn I, Meyerowitz J, Levit Kaplan A, Lyu J, Cheng Z, Tarkhanova OO, Moroz YS, Irwin JJ, Chang W, Shoichet BK, Skiniotis G| | PubMed
  27. Large library docking for cannabinoid-1 receptor agonists with reduced side effects.
    Tummino TA, Iliopoulos-Tsoutsouvas C, Braz JM, O'Brien ES, Stein RM, Craik V, Tran NK, Ganapathy S, Liu F, Shiimura Y, Tong F, Ho TC, Radchenko DS, Moroz YS, Rosado SR, Bhardwaj K, Benitez J, Liu Y, Kandasamy H, Normand C, Semache M, Sabbagh L, Glenn I, Irwin JJ, Kumar KK, Makriyannis A, Basbaum AI, Shoichet BK| | PubMed
  28. Docking for Molecules That Bind in a Symmetric Stack with SymDOCK.
    Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK| | PubMed
  29. Docking for EP4R antagonists active against inflammatory pain.
    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| | PubMed
  30. Preparing for the next pandemic.
    Shoichet BK, Craik CS| | PubMed
  31. Colloidal aggregation confounds cell-based Covid-19 antiviral screens.
    Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK| | PubMed
  32. Docking for molecules that bind in a symmetric stack with SymDOCK.
    Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK| | PubMed
  33. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
    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, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ| | PubMed
  34. Cryo-EM structure of Alzheimer's disease tau filaments with PET ligand MK-6240.
    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| | PubMed
  35. Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase.
    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| | PubMed
  36. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.
    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 LM, Lorenzo-Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García-Sastre A, Shoichet BK, Craik CS| | PubMed
  37. Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.
    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 A, Jin J, Fujimori DG, Irwin JJ, Vedadi M, Shoichet BK| | PubMed
  38. Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.
    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, Shoichet BK, Rudnick G| | PubMed
  39. Synthetic Ionizable Colloidal Drug Aggregates Enable Endosomal Disruption.
    Donders EN, Slaughter KV, Dank C, Ganesh AN, Shoichet BK, Lautens M, Shoichet MS| | PubMed
  40. Modeling the expansion of virtual screening libraries.
    Lyu J, Irwin JJ, Shoichet BK| | PubMed
  41. Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2.
    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| | PubMed
  42. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
    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, Ashworth A, Ahel I, Shoichet BK, Fraser JS| | PubMed
  43. Ligand recognition and allosteric modulation of the human MRGPRX1 receptor.
    Liu Y, Cao C, Huang XP, Gumpper RH, Rachman MM, Shih SL, Krumm BE, Zhang S, Shoichet BK, Fay JF, Roth BL| | PubMed
  44. Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor.
    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, Bouvier M, Du Y, Shoichet BK, Basbaum AI, Gmeiner P| | PubMed
  45. Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity.
    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 MJ, Panova O, Seven AB, Wetsel AQ, Wetsel WC, Irwin JJ, Skiniotis G, Shoichet BK, Roth BL, Ellman JA| | PubMed
  46. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2.
    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, Ashworth A, Ahel I, Shoichet BK, Fraser JS| | PubMed
  47. Inactive and active state structures template selective tools for the human 5-HT5A receptor.
    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| | PubMed
  48. Drug building blocks and libraries at risk in Ukraine.
    Kondratov IS, Moroz YS, Irwin JJ, Shoichet BK| | PubMed
  49. Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor.
    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| | PubMed
  50. Identification of a conserved drug binding pocket in TMEM16 proteins.
    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| | PubMed
  51. Publisher Correction: A practical guide to large-scale docking.
    Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK| | PubMed
  52. Structures of the σ2 receptor enable docking for bioactive ligand discovery.
    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| | PubMed
  53. Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens.
    O'Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK| | PubMed
  54. Structure, function and pharmacology of human itch GPCRs.
    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, Kim K, Karpiak J, Jan LY, Abraham SN, Jin J, Shoichet BK, Fay JF, Roth BL| | PubMed
  55. Efficient Exploration of Chemical Space with Docking and Deep Learning.
    Yang Y, Yao K, Repasky MP, Leswing K, Abel R, Shoichet BK, Jerome SV| | PubMed
  56. A practical guide to large-scale docking.
    Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK| | PubMed
  57. Energy penalties enhance flexible receptor docking in a model cavity.
    Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK| | PubMed
  58. Ligand Strain Energy in Large Library Docking.
    Gu S, Smith MS, Yang Y, Irwin JJ, Shoichet BK| | PubMed
  59. Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens.
    Oâ Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK| | PubMed
  60. Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.
    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, Galarneau JR, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK| | PubMed
  61. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
    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, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I| | PubMed
  62. A Crowding Barrier to Protein Inhibition in Colloidal Aggregates.
    Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK| | PubMed
  63. Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2.
    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 O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK| | PubMed
  64. Property-Unmatched Decoys in Docking Benchmarks.
    Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ| | PubMed
  65. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking.
    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, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Neto JB, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Johannes Gregor Matthias Rack, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I| | PubMed
  66. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
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  73. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
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  75. Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.
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  76. Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP.
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  77. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms.
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  78. GAIN domain-mediated cleavage is required for activation of G protein-coupled receptor 56 (GPR56) by its natural ligands and a small-molecule agonist.
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  79. Protein Stability Effects in Aggregate-Based Enzyme Inhibition.
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  81. Structural identification of a hotspot on CFTR for potentiation.
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  83. Ultra-large library docking for discovering new chemotypes.
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  84. Far away from the lamppost.
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  85. Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists.
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  86. The Recognition of Unrelated Ligands by Identical Proteins.
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  87. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
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  88. Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets.
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  90. Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor.
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  91. Prediction of enzymatic pathways by integrative pathway mapping.
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  92. Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone.
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  93. Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs.
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  94. Structure-Based Design and Discovery of New M2 Receptor Agonists.
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  95. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.
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  96. Discovery of new GPCR ligands to illuminate new biology.
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  97. Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets.
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  113. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.
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  115. Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65.
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  116. Corrigendum: The promise and peril of chemical probes.
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  117. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.
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  118. The Recognition of Identical Ligands by Unrelated Proteins.
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  119. Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.
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  120. Prediction and validation of enzyme and transporter off-targets for metformin.
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  121. An Aggregation Advisor for Ligand Discovery.
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  122. Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents.
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  124. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.
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  125. Homologous ligands accommodated by discrete conformations of a buried cavity.
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  126. Erratum: Covalent docking of large libraries for the discovery of chemical probes.
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  127. Colloidal aggregation and the in vitro activity of traditional Chinese medicines.
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  128. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.
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  129. Covalent docking of large libraries for the discovery of chemical probes.
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  130. Actin is required for IFT regulation in Chlamydomonas reinhardtii.
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  131. 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.
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  132. Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative.
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  133. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
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  134. Increasing chemical space coverage by combining empirical and computational fragment screens.
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  135. Prediction of substrates for glutathione transferases by covalent docking.
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  136. Substrate deconstruction and the nonadditivity of enzyme recognition.
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  137. Large-scale identification and analysis of suppressive drug interactions.
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  138. Drug discovery: follow your lead.
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  139. Colloidal drug formulations can explain "bell-shaped" concentration-response curves.
    Owen SC, Doak AK, Ganesh AN, Nedyalkova L, McLaughlin CK, Shoichet BK, Shoichet MS| | PubMed
  140. In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding.
    Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K| | PubMed
  141. Ligand pose and orientational sampling in molecular docking.
    Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK| | PubMed
  142. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.
    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| | PubMed
  143. Structure-guided discovery of new deaminase enzymes.
    Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM| | PubMed
  144. Blind prediction of charged ligand binding affinities in a model binding site.
    Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA| | PubMed
  145. Muscarinic receptors as model targets and antitargets for structure-based ligand discovery.
    Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK| | PubMed
  146. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities.
    Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK| | PubMed
  147. Structure-based discovery of antagonists of nuclear receptor LRH-1.
    Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ| | PubMed
  148. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor.
    Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK| | PubMed
  149. The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition.
    Merski M, Shoichet BK| | PubMed
  150. Colloidal aggregation causes inhibition of G protein-coupled receptors.
    Sassano MF, Doak AK, Roth BL, Shoichet BK| | PubMed
  151. Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4).
    Cameron RT, Coleman RG, Day JP, Yalla KC, Houslay MD, Adams DR, Shoichet BK, Baillie GS| | PubMed
  152. A pharmacological organization of G protein-coupled receptors.
    Lin H, Sassano MF, Roth BL, Shoichet BK| | PubMed
  153. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.
    Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM| | PubMed
  154. Drug discovery: nature's pieces.
    Shoichet BK| | PubMed
  155. Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily.
    Ornelas A, Korczynska M, Ragumani S, Kumaran D, Narindoshvili T, Shoichet BK, Swaminathan S, Raushel FM| | PubMed
  156. Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo.
    Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F| | PubMed
  157. Engineering a model protein cavity to catalyze the Kemp elimination.
    Merski M, Shoichet BK| | PubMed
  158. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
    Mysinger MM, Carchia M, Irwin JJ, Shoichet BK| | PubMed
  159. Identifying mechanism-of-action targets for drugs and probes.
    Gregori-Puigjané E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK| | PubMed
  160. Large-scale prediction and testing of drug activity on side-effect targets.
    Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L| | PubMed
  161. Colloidal aggregation affects the efficacy of anticancer drugs in cell culture.
    Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK| | PubMed
  162. Structure-based drug screening for G-protein-coupled receptors.
    Shoichet BK, Kobilka BK| | PubMed
  163. Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4.
    Mysinger MM, Weiss DR, Ziarek JJ, Gravel S, Doak AK, Karpiak J, Heveker N, Shoichet BK, Volkman BF| | PubMed
  164. A chemical screen identifies class a g-protein coupled receptors as regulators of cilia.
    Avasthi P, Marley A, Lin H, Gregori-Puigjane E, Shoichet BK, von Zastrow M, Marshall WF| | PubMed
  165. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.
    Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM| | PubMed
  166. Chemical informatics and target identification in a zebrafish phenotypic screen.
    Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK| | PubMed
  167. Statistical potential for modeling and ranking of protein-ligand interactions.
    Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A| | PubMed
  168. The Enzyme Function Initiative.
    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| | PubMed
  169. Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
    Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK| | PubMed
  170. Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET.
    Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A| | PubMed
  171. A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets.
    Poncet-Montange G, St Martin SJ, Bogatova OV, Prusiner SB, Shoichet BK, Ghaemmaghami S| | PubMed
  172. Enzymatic deamination of the epigenetic base N-6-methyladenine.
    Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM| | PubMed
  173. The chemical basis of pharmacology.
    Keiser MJ, Irwin JJ, Shoichet BK| | PubMed
  174. Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as β-lactamase inhibitors.
    Eidam O, Romagnoli C, Caselli E, Babaoglu K, Pohlhaus DT, Karpiak J, Bonnet R, Shoichet BK, Prati F| | PubMed
  175. The presynaptic component of the serotonergic system is required for clozapine's efficacy.
    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| | PubMed
  176. Rapid context-dependent ligand desolvation in molecular docking.
    Mysinger MM, Shoichet BK| | PubMed
  177. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.
    Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK| | PubMed
  178. Colloid formation by drugs in simulated intestinal fluid.
    Doak AK, Wille H, Prusiner SB, Shoichet BK| | PubMed
  179. Structure-based discovery of A2A adenosine receptor ligands.
    Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA| | PubMed
  180. Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.
    Tondi D, Calò S, Shoichet BK, Costi MP| | PubMed
  181. Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.
    DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD| | PubMed
  182. The hunt for 8-oxoguanine deaminase.
    Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM| | PubMed
  183. Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
    Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM| | PubMed
  184. Rapid behavior-based identification of neuroactive small molecules in the zebrafish.
    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| | PubMed
  185. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB.
    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| | PubMed
  186. Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease.
    Jadhav A, Ferreira RS, Klumpp C, Mott BT, Austin CP, Inglese J, Thomas CJ, Maloney DJ, Shoichet BK, Simeonov A| | PubMed
  187. Structural bases for stability-function tradeoffs in antibiotic resistance.
    Thomas VL, McReynolds AC, Shoichet BK| | PubMed
  188. Molecular docking screens using comparative models of proteins.
    Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A| | PubMed
  189. Predicting new molecular targets for known drugs.
    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| | PubMed
  190. Crystal structures of penicillin-binding protein 6 from Escherichia coli.
    Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK| | PubMed
  191. Automated docking screens: a feasibility study.
    Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y| | PubMed
  192. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
    Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK| | PubMed
  193. Docking and chemoinformatic screens for new ligands and targets.
    Kolb P, Ferreira RS, Irwin JJ, Shoichet BK| | PubMed
  194. Divergent modes of enzyme inhibition in a homologous structure-activity series.
    Ferreira RS, Bryant C, Ang KK, McKerrow JH, Shoichet BK, Renslo AR| | PubMed
  195. Quantifying biogenic bias in screening libraries.
    Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK| | PubMed
  196. Docking for fragment inhibitors of AmpC beta-lactamase.
    Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK| | PubMed
  197. Promiscuous aggregate-based inhibitors promote enzyme unfolding.
    Coan KE, Maltby DA, Burlingame AL, Shoichet BK| | PubMed
  198. Structure-based discovery of beta2-adrenergic receptor ligands.
    Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK| | PubMed
  199. Molecular docking and ligand specificity in fragment-based inhibitor discovery.
    Chen Y, Shoichet BK| | PubMed
  200. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily.
    Xiang DF, Kolb P, Fedorov AA, Meier MM, Fedorov LV, Nguyen TT, Sterner R, Almo SC, Shoichet BK, Raushel FM| | PubMed
  201. Re-examining the role of Lys67 in class C beta-lactamase catalysis.
    Chen Y, McReynolds A, Shoichet BK| | PubMed
  202. Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase.
    Marciano DC, Pennington JM, Wang X, Wang J, Chen Y, Thomas VL, Shoichet BK, Palzkill T| | PubMed
  203. Exploiting ordered waters in molecular docking.
    Huang N, Shoichet BK| | PubMed
  204. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors.
    Coan KE, Shoichet BK| | PubMed
  205. Quantifying the relationships among drug classes.
    Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK| | PubMed
  206. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
    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| | PubMed
  207. Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
    Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK| | PubMed
  208. Small-molecule aggregates inhibit amyloid polymerization.
    Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK| | PubMed
  209. Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors.
    Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F| | PubMed
  210. Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy.
    Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G, Shoichet BK, Costi MP| | PubMed
  211. Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases.
    Delmas J, Chen Y, Prati F, Robin F, Shoichet BK, Bonnet R| | PubMed
  212. No free energy lunch.
    Shoichet BK| | PubMed
  213. O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site.
    Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF| | PubMed
  214. Structure-based activity prediction for an enzyme of unknown function.
    Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM| | PubMed
  215. Predicting absolute ligand binding free energies to a simple model site.
    Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA| | PubMed
  216. Stability for function trade-offs in the enolase superfamily "catalytic module".
    Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC| | PubMed
  217. A high-throughput screen for aggregation-based inhibition in a large compound library.
    Feng BY, Simeonov A, Jadhav A, Babaoglu K, Inglese J, Shoichet BK, Austin CP| | PubMed
  218. The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution.
    Chen Y, Bonnet R, Shoichet BK| | PubMed
  219. An interview with Brian Shoichet, Ph.D. Professor, Department of Pharmaceutical Chemistry, University of California, San Francisco.
    Shoichet B| | PubMed
  220. Relating protein pharmacology by ligand chemistry.
    Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK| | PubMed
  221. Stability and equilibria of promiscuous aggregates in high protein milieus.
    Coan KE, Shoichet BK| | PubMed
  222. Interpreting steep dose-response curves in early inhibitor discovery.
    Shoichet BK| | PubMed
  223. Predicting substrates by docking high-energy intermediates to enzyme structures.
    Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK| | PubMed
  224. Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library.
    Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM| | PubMed
  225. Benchmarking sets for molecular docking.
    Huang N, Shoichet BK, Irwin JJ| | PubMed
  226. Deconstructing fragment-based inhibitor discovery.
    Babaoglu K, Shoichet BK| | PubMed
  227. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.
    Leach AR, Shoichet BK, Peishoff CE| | PubMed
  228. Screening in a spirit haunted world.
    Shoichet BK| | PubMed
  229. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures.
    Feng BY, Shoichet BK| | PubMed
  230. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.
    Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK| | PubMed
  231. Probing molecular docking in a charged model binding site.
    Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK| | PubMed
  232. A detergent-based assay for the detection of promiscuous inhibitors.
    Feng BY, Shoichet BK| | PubMed
  233. Virtual screening against metalloenzymes for inhibitors and substrates.
    Irwin JJ, Raushel FM, Shoichet BK| | PubMed
  234. Here be dragons: docking and screening in an uncharted region of chemical space.
    Brenk R, Irwin JJ, Shoichet BK| | PubMed
  235. Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase.
    Thomas VL, Golemi-Kotra D, Kim C, Vakulenko SB, Mobashery S, Shoichet BK| | PubMed
  236. High-throughput assays for promiscuous inhibitors.
    Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK| | PubMed
  237. Decoys for docking.
    Graves AP, Brenk R, Shoichet BK| | PubMed
  238. Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability.
    Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R| | PubMed
  239. Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases.
    Chen Y, Shoichet B, Bonnet R| | PubMed
  240. Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture.
    Tondi D, Morandi F, Bonnet R, Costi MP, Shoichet BK| | PubMed
  241. Hierarchical docking of databases of multiple ligand conformations.
    Lorber DM, Shoichet BK| | PubMed
  242. ZINC--a free database of commercially available compounds for virtual screening.
    Irwin JJ, Shoichet BK| | PubMed
  243. Virtual screening of chemical libraries.
    Shoichet BK| | PubMed
  244. Soft docking and multiple receptor conformations in virtual screening.
    Ferrari AM, Wei BQ, Costantino L, Shoichet BK| | PubMed
  245. Testing a flexible-receptor docking algorithm in a model binding site.
    Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK| | PubMed
  246. Allosteric inhibition through core disruption.
    Horn JR, Shoichet BK| | PubMed
  247. Thermodynamic cycle analysis and inhibitor design against beta-lactamase.
    Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK| | PubMed
  248. Identification and prediction of promiscuous aggregating inhibitors among known drugs.
    Seidler J, McGovern SL, Doman TN, Shoichet BK| | PubMed
  249. A specific mechanism of nonspecific inhibition.
    McGovern SL, Helfand BT, Feng B, Shoichet BK| | PubMed
  250. Structural aspects for evolution of beta-lactamases from penicillin-binding proteins.
    Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S| | PubMed
  251. Recognition and resistance in TEM beta-lactamase.
    Wang X, Minasov G, Blázquez J, Caselli E, Prati F, Shoichet BK| | PubMed
  252. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.
    McGovern SL, Shoichet BK| | PubMed
  253. Kinase inhibitors: not just for kinases anymore.
    McGovern SL, Shoichet BK| | PubMed
  254. Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough.
    Soelaiman S, Wei BQ, Bergson P, Lee YS, Shen Y, Mrksich M, Shoichet BK, Tang WJ| | PubMed
  255. A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase.
    Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS| | PubMed
  256. Nanomolar inhibitors of AmpC beta-lactamase.
    Morandi F, Caselli E, Morandi S, Focia PJ, Blázquez J, Shoichet BK, Prati F| | PubMed
  257. Structural basis for imipenem inhibition of class C beta-lactamases.
    Beadle BM, Shoichet BK| | PubMed
  258. A model binding site for testing scoring functions in molecular docking.
    Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK| | PubMed
  259. Using steric hindrance to design new inhibitors of class C beta-lactamases.
    Trehan I, Morandi F, Blaszczak LC, Shoichet BK| | PubMed
  260. Structural bases of stability-function tradeoffs in enzymes.
    Beadle BM, Shoichet BK| | PubMed
  261. Lead discovery using molecular docking.
    Shoichet BK, McGovern SL, Wei B, Irwin JJ| | PubMed
  262. Structure-based approach for binding site identification on AmpC beta-lactamase.
    Powers RA, Shoichet BK| | PubMed
  263. Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.
    Powers RA, Morandi F, Shoichet BK| | PubMed
  264. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.
    Wang X, Minasov G, Shoichet BK| | PubMed
  265. The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34.
    Wang X, Minasov G, Shoichet BK| | PubMed
  266. Protein-protein docking with multiple residue conformations and residue substitutions.
    Lorber DM, Udo MK, Shoichet BK| | PubMed
  267. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.
    Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK| | PubMed
  268. An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation.
    Minasov G, Wang X, Shoichet BK| | PubMed
  269. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening.
    McGovern SL, Caselli E, Grigorieff N, Shoichet BK| | PubMed
  270. Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.
    Wang X, Minasov G, Shoichet BK| | PubMed
  271. Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
    Beadle BM, Trehan I, Focia PJ, Shoichet BK| | PubMed
  272. Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design.
    Powers RA, Caselli E, Focia PJ, Prati F, Shoichet BK| | PubMed
  273. Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.
    Trehan I, Beadle BM, Shoichet BK| | PubMed
  274. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation.
    Beadle BM, Nicholas RA, Shoichet BK| | PubMed
  275. Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase.
    Tondi D, Powers RA, Caselli E, Negri MC, Blázquez J, Costi MP, Shoichet BK| | PubMed
  276. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation.
    Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK| | PubMed
  277. Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.
    Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK| | PubMed
  278. The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
    Powers RA, Blázquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK| | PubMed
  279. Functional analyses of AmpC beta-lactamase through differential stability.
    Beadle BM, McGovern SL, Patera A, Shoichet BK| | PubMed
  280. Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase.
    Tondi D, Slomczynska U, Costi MP, Watterson DM, Ghelli S, Shoichet BK| | PubMed
  281. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme.
    Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK| | PubMed
  282. Structure-based design of inhibitors specific for bacterial thymidylate synthase.
    Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP| | PubMed
  283. Ligand solvation in molecular docking.
    Shoichet BK, Leach AR, Kuntz ID| | PubMed
  284. 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.
    Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ| | PubMed
  285. Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase.
    Weston GS, Blázquez J, Baquero F, Shoichet BK| | PubMed
  286. An extended-spectrum AmpC-type beta-lactamase obtained by in vitro antibiotic selection.
    Morosini MI, Negri MC, Shoichet B, Baquero MR, Baquero F, Blázquez J| | PubMed
  287. Flexible ligand docking using conformational ensembles.
    Lorber DM, Shoichet BK| | PubMed
  288. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.
    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| | PubMed
  289. Predicting the structure of protein complexes: a step in the right direction.
    Shoichet BK, Kuntz ID| | PubMed
  290. Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive.
    Zhang XJ, Baase WA, Shoichet BK, Wilson KP, Matthews BW| | PubMed
  291. A relationship between protein stability and protein function.
    Shoichet BK, Baase WA, Kuroki R, Matthews BW| | PubMed
  292. Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion.
    Schellenberger U, Balaram P, Francis VS, Shoichet BK, Santi DV| | PubMed
  293. Matching chemistry and shape in molecular docking.
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