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
- Docking Screens for Novel Ligands Conferring New Biology.Irwin JJ, Shoichet BK| | PubMed
- In Vitro and In Vivo Characterization of the Alkaloid Nuciferine.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, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL| | PubMed
- Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS| | PubMed
- Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.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| | PubMed
- Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65.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| | PubMed
- Corrigendum: The promise and peril of chemical probes.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 D, Edwards AM, Frederiksen M, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Ross R, Roth B, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ| | PubMed
- Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA| | PubMed
- The Recognition of Identical Ligands by Unrelated Proteins.Barelier S, Sterling T, O'Meara MJ, Shoichet BK| | PubMed
- Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.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| | PubMed
- Prediction and validation of enzyme and transporter off-targets for metformin.Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM| | PubMed
296
MOST RECENT PUBLICATIONS FROM A TOTAL OF 296
- A Database for Large-Scale Docking and Experimental Results.Hall BW, Tummino TA, Tang K, Mailhot O, Castanon M, Irwin JJ, Shoichet BK| | PubMed
- 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
- 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
- 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
- A database for large-scale docking and experimental results.Hall BW, Tummino TA, Tang K, Irwin JJ, Shoichet BK| | PubMed
- A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils.Smith MS, DeGrado WF, Grabe M, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Colloidal Aggregation Confounds Cell-Based Covid-19 Antiviral Screens.Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Preparing for the next pandemic.Shoichet BK, Craik CS| | PubMed
- Colloidal aggregation confounds cell-based Covid-19 antiviral screens.Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Synthetic Ionizable Colloidal Drug Aggregates Enable Endosomal Disruption.Donders EN, Slaughter KV, Dank C, Ganesh AN, Shoichet BK, Lautens M, Shoichet MS| | PubMed
- Modeling the expansion of virtual screening libraries.Lyu J, Irwin JJ, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Drug building blocks and libraries at risk in Ukraine.Kondratov IS, Moroz YS, Irwin JJ, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens.O'Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK| | PubMed
- 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
- 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
- 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
- Energy penalties enhance flexible receptor docking in a model cavity.Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK| | PubMed
- Ligand Strain Energy in Large Library Docking.Gu S, Smith MS, Yang Y, Irwin JJ, Shoichet BK| | PubMed
- Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens.Oâ Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK| | PubMed
- 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
- 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
- A Crowding Barrier to Protein Inhibition in Colloidal Aggregates.Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK| | PubMed
- 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
- 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
- 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
- Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.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 M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ| | PubMed
- Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor.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| | PubMed
- Differential Roles of Extracellular Histidine Residues of GPR68 for Proton-Sensing and Allosteric Modulation by Divalent Metal Ions.Huang XP, Kenakin TP, Gu S, Shoichet BK, Roth BL| | PubMed
- The activities of drug inactive ingredients on biological targets.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, Shoichet BK, Urban L| | PubMed
- The Global Phosphorylation Landscape of SARS-CoV-2 Infection.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 M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ| | PubMed
- Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives.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| | PubMed
- An allosteric modulator binds to a conformational hub in the β2 adrenergic receptor.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| | PubMed
- A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.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, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ| | PubMed
- A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Wankowicz SA, Bohn M, Sharp PP, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Ashworth A, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ| | PubMed
- Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.Wan X, Yang T, Cuesta A, Pang X, Balius TE, Irwin JJ, Shoichet BK, Taunton J| | PubMed
- Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP.Zou L, Pottel J, Khuri N, Ngo HX, Ni Z, Tsakalozou E, Warren MS, Huang Y, Shoichet BK, Giacomini KM| | PubMed
- Virtual discovery of melatonin receptor ligands to modulate circadian rhythms.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| | PubMed
- GAIN domain-mediated cleavage is required for activation of G protein-coupled receptor 56 (GPR56) by its natural ligands and a small-molecule agonist.Zhu B, Luo R, Jin P, Li T, Oak HC, Giera S, Monk KR, Lak P, Shoichet BK, Piao X| | PubMed
- Protein Stability Effects in Aggregate-Based Enzyme Inhibition.Torosyan H, Shoichet BK| | PubMed
- Triggered Release Enhances the Cytotoxicity of Stable Colloidal Drug Aggregates.Donders EN, Ganesh AN, Torosyan H, Lak P, Shoichet BK, Shoichet MS| | PubMed
- Structural identification of a hotspot on CFTR for potentiation.Liu F, Zhang Z, Levit A, Levring J, Touhara KK, Shoichet BK, Chen J| | PubMed
- Colloidal Drug Aggregate Stability in High Serum Conditions and Pharmacokinetic Consequence.Ganesh AN, Aman A, Logie J, Barthel BL, Cogan P, Al-Awar R, Koch TH, Shoichet BK, Shoichet MS| | PubMed
- Ultra-large library docking for discovering new chemotypes.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| | PubMed
- Far away from the lamppost.Oprea TI, Jan L, Johnson GL, Roth BL, Ma'ayan A, Schürer S, Shoichet BK, Sklar LA, McManus MT| | PubMed
- Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists.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, Gmeiner P| | PubMed
- The Recognition of Unrelated Ligands by Identical Proteins.Pottel J, Levit A, Korczynska M, Fischer M, Shoichet BK| | PubMed
- The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.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, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ| | PubMed
- Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets.Weiss DR, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK| | PubMed
- Colloidal aggregation: from screening nuisance to formulation nuance.Ganesh AN, Donders EN, Shoichet BK, Shoichet MS| | PubMed
- Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor.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| | PubMed
- Prediction of enzymatic pathways by integrative pathway mapping.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, Shoichet BK, Sali A| | PubMed
- Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone.Wang S, Che T, Levit A, Shoichet BK, Wacker D, Roth BL| | PubMed
- Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs.McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL| | PubMed
- Structure-Based Design and Discovery of New M2 Receptor Agonists.Fish I, Stößel A, Eitel K, Valant C, Albold S, Huebner H, Möller D, Clark MJ, Sunahara RK, Christopoulos A, Shoichet BK, Gmeiner P| | PubMed
- D4 dopamine receptor high-resolution structures enable the discovery of selective agonists.Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL| | PubMed
- Discovery of new GPCR ligands to illuminate new biology.Roth BL, Irwin JJ, Shoichet BK| | PubMed
- Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets.Maciejewski M, Lounkine E, Whitebread S, Farmer P, DuMouchel W, Shoichet BK, Urban L| | PubMed
- Testing inhomogeneous solvation theory in structure-based ligand discovery.Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK| | PubMed
- Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations.Ganesh AN, Logie J, McLaughlin CK, Barthel BL, Koch TH, Shoichet BK, Shoichet MS| | PubMed
- A New Spin on Antibody-Drug Conjugates: Trastuzumab-Fulvestrant Colloidal Drug Aggregates Target HER2-Positive Cells.Ganesh AN, McLaughlin CK, Duan D, Shoichet BK, Shoichet MS| | PubMed
- In silico design of novel probes for the atypical opioid receptor MRGPRX2.Lansu K, Karpiak J, Liu J, Huang XP, McCorvy JD, Kroeze WK, Che T, Nagase H, Carroll FI, Jin J, Shoichet BK, Roth BL| | PubMed
- Crystal Structure of an LSD-Bound Human Serotonin Receptor.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| | PubMed
- Internal Structure and Preferential Protein Binding of Colloidal Aggregates.Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK| | PubMed
- Design, Synthesis, and Biological Evaluation of Novel Tetrahydroprotoberberine Derivatives (THPBs) as Selective α1A-Adrenoceptor Antagonists.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| | PubMed
- A Molecular Basis for Innovation in Drug Excipients.Irwin JJ, Pottel J, Zou L, Wen H, Zuk S, Zhang X, Sterling T, Shoichet BK, Lionberger R, Giacomini KM| | PubMed
- Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.Lee H, Fischer M, Shoichet BK, Liu SY| | PubMed
- Structure-based discovery of opioid analgesics with reduced side effects.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| | PubMed
- Identification of Novel Smoothened Ligands Using Structure-Based Docking.Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S| | PubMed
- Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.O'Meara MJ, Ballouz S, Shoichet BK, Gillis J| | PubMed
- Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward.Shoichet BK, Walters WP, Jiang H, Bajorath J| | PubMed
- Docking Screens for Novel Ligands Conferring New Biology.Irwin JJ, Shoichet BK| | PubMed
- In Vitro and In Vivo Characterization of the Alkaloid Nuciferine.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, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL| | PubMed
- Stable Colloidal Drug Aggregates Catch and Release Active Enzymes.McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS| | PubMed
- Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.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| | PubMed
- Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65.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| | PubMed
- Corrigendum: The promise and peril of chemical probes.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 D, Edwards AM, Frederiksen M, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Ross R, Roth B, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ| | PubMed
- Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking.Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA| | PubMed
- The Recognition of Identical Ligands by Unrelated Proteins.Barelier S, Sterling T, O'Meara MJ, Shoichet BK| | PubMed
- Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.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| | PubMed
- Prediction and validation of enzyme and transporter off-targets for metformin.Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM| | PubMed
- An Aggregation Advisor for Ligand Discovery.Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK| | PubMed
- Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents.Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL| | PubMed
- The promise and peril of chemical probes.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 D, Edwards AM, Frederiksen M, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Roth B, Roth B, Ross R, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ| | PubMed
- One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.Fischer M, Shoichet BK, Fraser JS| | PubMed
- Homologous ligands accommodated by discrete conformations of a buried cavity.Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK| | PubMed
- Erratum: Covalent docking of large libraries for the discovery of chemical probes.London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J| | PubMed
- Colloidal aggregation and the in vitro activity of traditional Chinese medicines.Duan D, Doak AK, Nedyalkova L, Shoichet BK| | PubMed
- Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK| | PubMed
- Covalent docking of large libraries for the discovery of chemical probes.London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J| | PubMed
- Actin is required for IFT regulation in Chlamydomonas reinhardtii.Avasthi P, Onishi M, Karpiak J, Yamamoto R, Mackinder L, Jonikas MC, Sale WS, Shoichet B, Pringle JR, Marshall WF| | PubMed
- 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.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| | PubMed
- Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative.Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP| | PubMed
- Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.Fischer M, Coleman RG, Fraser JS, Shoichet BK| | PubMed
- Increasing chemical space coverage by combining empirical and computational fragment screens.Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G| | PubMed
- Prediction of substrates for glutathione transferases by covalent docking.Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A| | PubMed
- Substrate deconstruction and the nonadditivity of enzyme recognition.Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK| | PubMed
- Large-scale identification and analysis of suppressive drug interactions.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| | PubMed
- Drug discovery: follow your lead.Shoichet BK| | PubMed
- 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
- 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
- Ligand pose and orientational sampling in molecular docking.Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition.Merski M, Shoichet BK| | PubMed
- Colloidal aggregation causes inhibition of G protein-coupled receptors.Sassano MF, Doak AK, Roth BL, Shoichet BK| | PubMed
- 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
- A pharmacological organization of G protein-coupled receptors.Lin H, Sassano MF, Roth BL, Shoichet BK| | PubMed
- 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
- Drug discovery: nature's pieces.Shoichet BK| | PubMed
- 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
- 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
- Engineering a model protein cavity to catalyze the Kemp elimination.Merski M, Shoichet BK| | PubMed
- Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.Mysinger MM, Carchia M, Irwin JJ, Shoichet BK| | PubMed
- 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
- 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
- Colloidal aggregation affects the efficacy of anticancer drugs in cell culture.Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK| | PubMed
- Structure-based drug screening for G-protein-coupled receptors.Shoichet BK, Kobilka BK| | PubMed
- 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
- 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
- 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
- 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
- Statistical potential for modeling and ranking of protein-ligand interactions.Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A| | PubMed
- 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
- 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
- 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
- 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
- Enzymatic deamination of the epigenetic base N-6-methyladenine.Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM| | PubMed
- The chemical basis of pharmacology.Keiser MJ, Irwin JJ, Shoichet BK| | PubMed
- 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
- 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
- Rapid context-dependent ligand desolvation in molecular docking.Mysinger MM, Shoichet BK| | PubMed
- 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
- Colloid formation by drugs in simulated intestinal fluid.Doak AK, Wille H, Prusiner SB, Shoichet BK| | PubMed
- Structure-based discovery of A2A adenosine receptor ligands.Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA| | PubMed
- Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.Tondi D, Calò S, Shoichet BK, Costi MP| | PubMed
- Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs.DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD| | PubMed
- 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
- 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
- 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
- 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
- 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
- Structural bases for stability-function tradeoffs in antibiotic resistance.Thomas VL, McReynolds AC, Shoichet BK| | PubMed
- Molecular docking screens using comparative models of proteins.Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A| | PubMed
- 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
- 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
- Automated docking screens: a feasibility study.Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y| | PubMed
- 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
- Docking and chemoinformatic screens for new ligands and targets.Kolb P, Ferreira RS, Irwin JJ, Shoichet BK| | PubMed
- Divergent modes of enzyme inhibition in a homologous structure-activity series.Ferreira RS, Bryant C, Ang KK, McKerrow JH, Shoichet BK, Renslo AR| | PubMed
- Quantifying biogenic bias in screening libraries.Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK| | PubMed
- Docking for fragment inhibitors of AmpC beta-lactamase.Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK| | PubMed
- Promiscuous aggregate-based inhibitors promote enzyme unfolding.Coan KE, Maltby DA, Burlingame AL, Shoichet BK| | PubMed
- Structure-based discovery of beta2-adrenergic receptor ligands.Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK| | PubMed
- Molecular docking and ligand specificity in fragment-based inhibitor discovery.Chen Y, Shoichet BK| | PubMed
- 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
- Re-examining the role of Lys67 in class C beta-lactamase catalysis.Chen Y, McReynolds A, Shoichet BK| | PubMed
- 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
- Exploiting ordered waters in molecular docking.Huang N, Shoichet BK| | PubMed
- Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors.Coan KE, Shoichet BK| | PubMed
- Quantifying the relationships among drug classes.Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK| | PubMed
- 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
- 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
- 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
- Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors.Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F| | PubMed
- 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
- 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
- No free energy lunch.Shoichet BK| | PubMed
- O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site.Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF| | PubMed
- 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
- Predicting absolute ligand binding free energies to a simple model site.Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA| | PubMed
- Stability for function trade-offs in the enolase superfamily "catalytic module".Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC| | PubMed
- 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
- The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution.Chen Y, Bonnet R, Shoichet BK| | PubMed
- An interview with Brian Shoichet, Ph.D. Professor, Department of Pharmaceutical Chemistry, University of California, San Francisco.Shoichet B| | PubMed
- Relating protein pharmacology by ligand chemistry.Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK| | PubMed
- Stability and equilibria of promiscuous aggregates in high protein milieus.Coan KE, Shoichet BK| | PubMed
- Interpreting steep dose-response curves in early inhibitor discovery.Shoichet BK| | PubMed
- Predicting substrates by docking high-energy intermediates to enzyme structures.Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK| | PubMed
- 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
- Benchmarking sets for molecular docking.Huang N, Shoichet BK, Irwin JJ| | PubMed
- Deconstructing fragment-based inhibitor discovery.Babaoglu K, Shoichet BK| | PubMed
- Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.Leach AR, Shoichet BK, Peishoff CE| | PubMed
- Screening in a spirit haunted world.Shoichet BK| | PubMed
- Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures.Feng BY, Shoichet BK| | PubMed
- The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution.Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK| | PubMed
- Probing molecular docking in a charged model binding site.Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK| | PubMed
- A detergent-based assay for the detection of promiscuous inhibitors.Feng BY, Shoichet BK| | PubMed
- Virtual screening against metalloenzymes for inhibitors and substrates.Irwin JJ, Raushel FM, Shoichet BK| | PubMed
- Here be dragons: docking and screening in an uncharted region of chemical space.Brenk R, Irwin JJ, Shoichet BK| | PubMed
- 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
- High-throughput assays for promiscuous inhibitors.Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK| | PubMed
- Decoys for docking.Graves AP, Brenk R, Shoichet BK| | PubMed
- 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
- Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases.Chen Y, Shoichet B, Bonnet R| | PubMed
- 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
- Hierarchical docking of databases of multiple ligand conformations.Lorber DM, Shoichet BK| | PubMed
- ZINC--a free database of commercially available compounds for virtual screening.Irwin JJ, Shoichet BK| | PubMed
- Virtual screening of chemical libraries.Shoichet BK| | PubMed
- Soft docking and multiple receptor conformations in virtual screening.Ferrari AM, Wei BQ, Costantino L, Shoichet BK| | PubMed
- Testing a flexible-receptor docking algorithm in a model binding site.Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK| | PubMed
- Allosteric inhibition through core disruption.Horn JR, Shoichet BK| | PubMed
- Thermodynamic cycle analysis and inhibitor design against beta-lactamase.Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK| | PubMed
- Identification and prediction of promiscuous aggregating inhibitors among known drugs.Seidler J, McGovern SL, Doman TN, Shoichet BK| | PubMed
- A specific mechanism of nonspecific inhibition.McGovern SL, Helfand BT, Feng B, Shoichet BK| | PubMed
- Structural aspects for evolution of beta-lactamases from penicillin-binding proteins.Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S| | PubMed
- Recognition and resistance in TEM beta-lactamase.Wang X, Minasov G, Blázquez J, Caselli E, Prati F, Shoichet BK| | PubMed
- Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.McGovern SL, Shoichet BK| | PubMed
- Kinase inhibitors: not just for kinases anymore.McGovern SL, Shoichet BK| | PubMed
- 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
- 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
- Nanomolar inhibitors of AmpC beta-lactamase.Morandi F, Caselli E, Morandi S, Focia PJ, Blázquez J, Shoichet BK, Prati F| | PubMed
- Structural basis for imipenem inhibition of class C beta-lactamases.Beadle BM, Shoichet BK| | PubMed
- A model binding site for testing scoring functions in molecular docking.Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK| | PubMed
- Using steric hindrance to design new inhibitors of class C beta-lactamases.Trehan I, Morandi F, Blaszczak LC, Shoichet BK| | PubMed
- Structural bases of stability-function tradeoffs in enzymes.Beadle BM, Shoichet BK| | PubMed
- Lead discovery using molecular docking.Shoichet BK, McGovern SL, Wei B, Irwin JJ| | PubMed
- Structure-based approach for binding site identification on AmpC beta-lactamase.Powers RA, Shoichet BK| | PubMed
- Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.Powers RA, Morandi F, Shoichet BK| | PubMed
- Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs.Wang X, Minasov G, Shoichet BK| | PubMed
- 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
- Protein-protein docking with multiple residue conformations and residue substitutions.Lorber DM, Udo MK, Shoichet BK| | PubMed
- 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
- 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
- A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening.McGovern SL, Caselli E, Grigorieff N, Shoichet BK| | PubMed
- Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.Wang X, Minasov G, Shoichet BK| | PubMed
- 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
- 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
- Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.Trehan I, Beadle BM, Shoichet BK| | PubMed
- Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation.Beadle BM, Nicholas RA, Shoichet BK| | PubMed
- 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
- 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
- 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
- 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
- Functional analyses of AmpC beta-lactamase through differential stability.Beadle BM, McGovern SL, Patera A, Shoichet BK| | PubMed
- 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
- Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme.Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK| | PubMed
- 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
- Ligand solvation in molecular docking.Shoichet BK, Leach AR, Kuntz ID| | PubMed
- 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
- Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase.Weston GS, Blázquez J, Baquero F, Shoichet BK| | PubMed
- 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
- Flexible ligand docking using conformational ensembles.Lorber DM, Shoichet BK| | PubMed
- 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
- Predicting the structure of protein complexes: a step in the right direction.Shoichet BK, Kuntz ID| | PubMed
- 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
- A relationship between protein stability and protein function.Shoichet BK, Baase WA, Kuroki R, Matthews BW| | PubMed
- 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
- Matching chemistry and shape in molecular docking.Shoichet BK, Kuntz ID| | PubMed
- Structure-based discovery of inhibitors of thymidylate synthase.Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM| | PubMed
- Protein docking and complementarity.Shoichet BK, Kuntz ID| | PubMed
- Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis.Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P| | PubMed