Last updated on: Saturday 2024-12-21 12:16:17 PM
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. High-affinity agonists reveal recognition motifs for the MRGPRD GPCR. Cell Rep. 2024 Nov 23; 43(12):114942. [PubMed] [DOI]
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. Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning. bioRxiv. 2024 Aug 26. [PubMed] [DOI]
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. Large library docking identifies positive allosteric modulators of the calcium-sensing receptor. Science. 2024 Sep 20; 385(6715):eado1868. [PubMed] [DOI]
Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Zapatero-Belinchón FJ, McCavitt-Malvido M, Doruk YU, Stevens MGV, Diolati 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. The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2. bioRxiv. 2024 Aug 09. [PubMed] [DOI]
Slaughter KV, Donders EN, Jones MS, Sabbah SG, Elliott MJ, Shoichet BK, Cescon DW, Shoichet MS. Ionizable Drugs Enable Intracellular Delivery of Co-Formulated siRNA. Adv Mater. 2024 Aug 15; e2403701. [PubMed] [DOI]
Wu Y, Liu F, Glenn I, Fonseca-Valencia K, Paris L, Xiong Y, Jerome SV, Brooks CL, Shoichet BK. Identifying Artifacts from Large Library Docking. bioRxiv. 2024 Jul 18. [PubMed] [DOI]
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. The impact of Library Size and Scale of Testing on Virtual Screening. bioRxiv. 2024 Jul 11. [PubMed] [DOI]
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. Discovery of Protease-Activated Receptor 4 (PAR4)-Tethered Ligand Antagonists Using Ultralarge Virtual Screening. ACS Pharmacol Transl Sci. 2024 Apr 12; 7(4):1086-1100. [PubMed] [DOI]
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. AlphaFold2 structures guide prospective ligand discovery. Science. 2024 Jun 21; 384(6702):eadn6354. [PubMed] [DOI]
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. Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor. bioRxiv. 2024 Mar 06. [PubMed] [DOI]
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. Profiling the proximal proteome of the activated μ-opioid receptor. Nat Chem Biol. 2024 Mar 25. [PubMed] [DOI]
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. Large library docking for cannabinoid-1 receptor agonists with reduced side effects. bioRxiv. 2024 Jan 23. [PubMed] [DOI]
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. Structure-based discovery of positive allosteric modulators for the calcium sensing receptor. bioRxiv. 2023 Dec 27. [PubMed] [DOI]
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. AlphaFold2 structures template ligand discovery. bioRxiv. 2023 Dec 21. [PubMed] [DOI]
Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK. Docking for molecules that bind in a symmetric stack with SymDOCK. bioRxiv. 2023 Oct 29. [PubMed] [DOI]
Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal aggregation confounds cell-based Covid-19 antiviral screens. bioRxiv. 2023 Oct 30. [PubMed] [DOI]
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. Docking for EP4R antagonists active against inflammatory pain. Nat Commun. 2023 Dec 06; 14(1):8067. [PubMed] [DOI]
Shoichet BK, Craik CS. Preparing for the next pandemic. Science. 2023 Nov 10; 382(6671):649-650. [PubMed] [DOI]
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. Cryo-EM structure of Alzheimer's disease tau filaments with PET ligand MK-6240. bioRxiv. 2023 Sep 22. [PubMed] [DOI]
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. Structure-based discovery of CFTR potentiators and inhibitors. bioRxiv. 2023 Sep 12. [PubMed] [DOI]
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. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun. 2023 Sep 27; 14(1):6030. [PubMed] [DOI]
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. Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase. Nat Commun. 2023 08 12; 14(1):4874. [PubMed] [DOI]
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. Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase. J Med Chem. 2023 06 22; 66(12):7785-7803. [PubMed] [DOI]
Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi T, 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 Y, Taunton J, Renslo AR, Irwin JJ, García-Sastre A, Shoichet BK, Craik CS. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci. 2023 Jun 24; e4712. [PubMed] [DOI]
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. Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Cell. 2023 May 11; 186(10):2160-2175.e17. [PubMed] [DOI]
Donders EN, Slaughter KV, Dank C, Ganesh AN, Shoichet BK, Lautens M, Shoichet MS. Synthetic Ionizable Colloidal Drug Aggregates Enable Endosomal Disruption. Adv Sci (Weinh). 2023 Mar 11; e2300311. [PubMed] [DOI]
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. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A. 2023 Jan 10; 120(2):e2212931120. [PubMed] [DOI]
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. Fluorogenic reporter enables identification of compounds that inhibit SARS-CoV-2. Nat Microbiol. 2023 Jan; 8(1):121-134. [PubMed] [DOI]
Lyu J, Irwin JJ, Shoichet BK. Modeling the expansion of virtual screening libraries. Nat Chem Biol. 2023 Jan 16. [PubMed] [DOI]
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. Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor. Science. 2022 09 30; 377(6614):eabn7065. [PubMed] [DOI]
Kaplan AL, Confair DN, Kim K, Barros-?lvarez 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. Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity. Nature. 2022 10; 610(7932):582-591. [PubMed] [DOI]
Fink EA, Xu J, H?bner 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. Structure-based discovery of nonopioid analgesics acting through the a2A-adrenergic receptor. Science. 2022 09 30; 377(6614):eabn7065. [PubMed] [DOI]
Liu Y, Cao C, Huang XP, Gumpper RH, Rachman MM, Shih SL, Krumm BE, Zhang S, Shoichet BK, Fay JF, Roth BL. Ligand recognition and allosteric modulation of the human MRGPRX1 receptor. Nat Chem Biol. 2022 Oct 27. [PubMed] [DOI]
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. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv. 2022 Jul 28. [PubMed] [DOI]
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. Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv. 2022 Jun 28. [PubMed] [DOI]
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. Inactive and active state structures template selective tools for the human 5-HT5A receptor. Nat Struct Mol Biol. 2022 Jul; 29(7):677-687. [PubMed] [DOI]
Kondratov IS, Moroz YS, Irwin JJ, Shoichet BK. Drug building blocks and libraries at risk in Ukraine. Science. 2022 05 27; 376(6596):929. [PubMed] [DOI]
Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK. Publisher Correction: A practical guide to large-scale docking. Nat Protoc. 2022 Jan; 17(1):177. [PubMed] [DOI]
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. Identification of a conserved drug binding pocket in TMEM16 proteins. Res Sq. 2022 Feb 10. [PubMed] [DOI]
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. Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor. J Med Chem. 2022 Mar 10; 65(5):4201-4217. [PubMed] [DOI]
O'Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK. Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens. J Med Chem. 2021 12 09; 64(23):17530-17539. [PubMed] [DOI]
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. Structures of the σ2 receptor enable docking for bioactive ligand discovery. Nature. 2021 Dec; 600(7890):759-764. [PubMed] [DOI]
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. Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2. bioRxiv. 2021 Mar 24. [PubMed] [DOI]
Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK. A practical guide to large-scale docking. Nat Protoc. 2021 10; 16(10):4799-4832. [PubMed] [DOI]
Yang Y, Yao K, Repasky MP, Leswing K, Abel R, Shoichet BK, Jerome SV. Efficient Exploration of Chemical Space with Docking and Deep Learning. J Chem Theory Comput. 2021 Nov 09; 17(11):7106-7119. [PubMed] [DOI]
Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK. Publisher Correction: A practical guide to large-scale docking. Nat Protoc. 2021 Dec 09. [PubMed] [DOI]
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. Structure, function and pharmacology of human itch GPCRs. Nature. 2021 Nov 17. [PubMed] [DOI]
Gu S, Smith MS, Yang Y, Irwin JJ, Shoichet BK. Ligand Strain Energy in Large Library Docking. J Chem Inf Model. 2021 Sep 01. [PubMed] [DOI]
Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proc Natl Acad Sci U S A. 2021 Sep 07; 118(36). [PubMed] [DOI]
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. Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2. Science. 2021 07 30; 373(6554):541-547. [PubMed] [DOI] [Almetric] [C&EN] [In the Pipeline] [Interview] [Liberation] [Pharmacology International]
Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 04; 7(16). [PubMed] [DOI]
Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK. A Crowding Barrier to Protein Inhibition in Colloidal Aggregates. J Med Chem. 2021 Mar 24. [PubMed] [DOI]
Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model. 2021 Jan 25. [PubMed] [DOI]
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, 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, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, 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. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. [PubMed] [DOI]
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. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468. [PubMed] [DOI]
Huang XP, Kenakin TP, Gu S, Shoichet BK, Roth BL. Differential Roles of Extracellular Histidine Residues of GPR68 for Proton-Sensing and Allosteric Modulation by Divalent Metal Ions. Biochemistry. 2020 09 29; 59(38):3594-3614. [PubMed] [DOI]
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. An allosteric modulator binds to a conformational hub in the β2 adrenergic receptor. Nat Chem Biol. 2020 07; 16(7):749-755. [PubMed] [DOI]
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, 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, Rack JGM, 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. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24. [PubMed] [DOI]
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. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Oct 15. [PubMed] [DOI]
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. Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor. Cell. 2020 Sep 17; 182(6):1574-1588.e19. [PubMed] [DOI]
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. The activities of drug inactive ingredients on biological targets. Science. 2020 07 24; 369(6502):403-413. [PubMed] [DOI] [PDF]
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. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 Jun 28. [PubMed] [DOI]
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. Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives. Proc Natl Acad Sci U S A. 2020 Jun 22. [PubMed] [DOI]
Wan X, Yang T, Cuesta A, Pang X, Balius TE, Irwin JJ, Shoichet BK, Taunton J. Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. J Am Chem Soc. 2020 Mar 04. [PubMed] [DOI]
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. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. 2020 Feb 10. [PubMed] [DOI] [UCSF News]
Zou L, Pottel J, Khuri N, Ngo HX, Ni Z, Tsakalozou E, Warren MS, Huang Y, Shoichet BK, Giacomini KM. Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP. Mol Pharm. 2020 Jan 28. [PubMed] [DOI]
Zhu B, Luo R, Jin P, Li T, Oak HC, Giera S, Monk KR, Lak P, Shoichet BK, Piao X. GAIN domain-mediated cleavage is required for activation of G protein-coupled receptor 56 (GPR56) by its natural ligands and a small-molecule agonist. J Biol Chem. 2019 Oct 18. [PubMed] [DOI] [Download PDF]
Torosyan H, Shoichet BK. Protein Stability Effects in Aggregate-Based Enzyme Inhibition. J Med Chem. 2019 Oct 17. [PubMed] [DOI] [Download PDF]
Ganesh AN, Aman A, Logie J, Barthel BL, Cogan P, Al-Awar R, Koch TH, Shoichet BK, Shoichet MS. Colloidal Drug Aggregate Stability in High Serum Conditions and Pharmacokinetic Consequence. ACS Chem Biol. 2019 Apr 19; 14(4):751-757. [PubMed] [DOI] [Download PDF]
Liu F, Zhang Z, Levit A, Levring J, Touhara KK, Shoichet BK, Chen J. Structural identification of a hotspot on CFTR for potentiation. Science. 2019 06 21; 364(6446):1184-1188. [PubMed] [DOI] [Download PDF]
Donders EN, Ganesh AN, Torosyan H, Lak P, Shoichet BK, Shoichet MS. Triggered Release Enhances the Cytotoxicity of Stable Colloidal Drug Aggregates. ACS Chem Biol. 2019 Jun 25. [PubMed] [DOI] [Download PDF]
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. Ultra-large library docking for discovering new chemotypes. Nature. 2019 Feb; 566(7743):224-229. [PubMed] [DOI] [BioCentury] [Commentary in Science] [Drug Target Review] [Faculty of 1000] [In the Pipeline] [NIH Press Release] [Nature Editorials] [Nature News and Views] [Pratical Fragments] [Spanish e-duque.net article] [Spanish mailchi.mp article] [UCSF News] [Download PDF]
Oprea TI, Jan L, Johnson GL, Roth BL, Ma'ayan A, Schürer S, Shoichet BK, Sklar LA, McManus MT. Far away from the lamppost. PLoS Biol. 2018 Dec; 16(12):e3000067. [PubMed] [DOI] [Download PDF]
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. Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists. Proc Natl Acad Sci U S A. 2018 11 20; 115(47):12046-12050. [PubMed] [DOI] [Download PDF]
Pottel J, Levit A, Korczynska M, Fischer M, Shoichet BK. The Recognition of Unrelated Ligands by Identical Proteins. ACS Chem Biol. 2018 Sep 21; 13(9):2522-2533. [PubMed] [DOI] [Download PDF]
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. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 Jul 26; 174(3):505-520. [PubMed] [DOI] [Psychiatric Cell Map Initiative] [Download PDF]
Weiss DR, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK. Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets. J Med Chem. 2018 Aug 09; 61(15):6830-6845. [PubMed] [DOI] [Download PDF]
Ganesh AN, Donders EN, Shoichet BK, Shoichet MS. Colloidal aggregation: from screening nuisance to formulation nuance. Nano Today. 2018 Apr; 19:188-200. [PubMed] [DOI] [Download PDF]
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. Structure-based discovery of selective positive allosteric modulators of antagonists for the M2 muscarinic acetylcholine receptor. Proc Natl Acad Sci U S A. 2018 03 06; 115(10):E2419-E2428. [PubMed] [DOI] [F1000] [Download PDF]
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. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 2018 01 29; 7. [PubMed] [DOI] [Download PDF]
Wang S, Che T, Levit A, Shoichet BK, Wacker D, Roth BL. Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone. Nature. 2018 03 08; 555(7695):269-273. [PubMed] [DOI] [PDB 6CM4] [Download PDF]
McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL. Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. Nat Chem Biol. 2018 02; 14(2):126-134. [PubMed] [DOI]
Fish I, Stößel A, Eitel K, Valant C, Albold S, Huebner H, Möller D, Clark MJ, Sunahara RK, Christopoulos A, Shoichet BK, Gmeiner P. Structure-Based Design and Discovery of New M2 Receptor Agonists. J Med Chem. 2017 11 22; 60(22):9239-9250. [PubMed] [DOI] [Download PDF]
Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science. 2017 10 20; 358(6361):381-386. [PubMed] [DOI] [PDB 5WIU] [PDB 5WIV] [UCSF News] [Download PDF]
Roth BL, Irwin JJ, Shoichet BK. Discovery of new GPCR ligands to illuminate new biology. Nat Chem Biol. 2017 Nov; 13(11):1143-1151. [PubMed] [DOI] [Download PDF]
Maciejewski M, Lounkine E, Whitebread S, Farmer P, DuMouchel W, Shoichet BK, Urban L. Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets. Elife. 2017 08 08; 6. [PubMed] [DOI] [Download PDF]
Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. Proc Natl Acad Sci U S A. 2017 08 15; 114(33):E6839-E6846. [PubMed] [DOI] [Download PDF]
Ganesh AN, Logie J, McLaughlin CK, Barthel BL, Koch TH, Shoichet BK, Shoichet MS. Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations. Mol Pharm. 2017 06 05; 14(6):1852-1860. [PubMed] [DOI] [Download PDF]
Ganesh AN, McLaughlin CK, Duan D, Shoichet BK, Shoichet MS. A New Spin on Antibody-Drug Conjugates: Trastuzumab-Fulvestrant Colloidal Drug Aggregates Target HER2-Positive Cells. ACS Appl Mater Interfaces. 2017 Apr 12; 9(14):12195-12202. [PubMed] [DOI] [Download PDF]
Kiessling LL, Kincaid VA, London N, Shoichet BK. Inhibitors of UDP-galactopyranose mutase. US Patent , 9708344 (2017)
Lansu K, Karpiak J, Liu J, Huang XP, McCorvy JD, Kroeze WK, Che T, Nagase H, Carroll FI, Jin J, Shoichet BK, Roth BL. In silico design of novel probes for the atypical opioid receptor MRGPRX2. Nat Chem Biol. 2017 05; 13(5):529-536. [PubMed] [DOI] [Download PDF]
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. Crystal Structure of an LSD-Bound Human Serotonin Receptor. Cell. 2017 01 26; 168(3):377-389.e12. [PubMed] [DOI] [F1000] [Nature NEWS] [Newsweek] [PDB 5TVN] [Scientific American] [Download PDF]
Duan D, Torosyan H, Elnatan D, McLaughlin CK, Logie J, Shoichet MS, Agard DA, Shoichet BK. Internal Structure and Preferential Protein Binding of Colloidal Aggregates. ACS Chem Biol. 2017 01 20; 12(1):282-290. [PubMed] [DOI] [Download PDF]
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. Design, Synthesis, and Biological Evaluation of Novel Tetrahydroprotoberberine Derivatives (THPBs) as Selective α1A-Adrenoceptor Antagonists. J Med Chem. 2016 Oct 27; 59(20):9489-9502. [PubMed] [DOI] [Download PDF]
Irwin JJ, Pottel J, Zou L, Wen H, Zuk S, Zhang X, Sterling T, Shoichet BK, Lionberger R, Giacomini KM. A Molecular Basis for Innovation in Drug Excipients. Clin Pharmacol Ther. 2017 03; 101(3):320-323. [PubMed] [DOI] [Download PDF]
Lee H, Fischer M, Shoichet BK, Liu SY. Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics. J Am Chem Soc. 2016 09 21; 138(37):12021-4. [PubMed] [DOI] [Download PDF]
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. Structure-based discovery of opioid analgesics with reduced side effects. Nature. 2016 09 08; 537(7619):185-190. [PubMed] [DOI] [BioCentury] [Download PDF]
Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S. Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One. 2016; 11(8):e0160365. [PubMed] [DOI] [Download PDF]
O'Meara MJ, Ballouz S, Shoichet BK, Gillis J. Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS One. 2016; 11(7):e0160098. [PubMed] [DOI] [Download PDF]
Shoichet BK, Walters WP, Jiang H, Bajorath J. Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward. J Med Chem. 2016 05 12; 59(9):4033-4. [PubMed] [DOI] [Download PDF]
Irwin JJ, Shoichet BK. Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 05 12; 59(9):4103-20. [PubMed] [DOI] [Download PDF]
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. In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. PLoS One. 2016; 11(3):e0150602. [PubMed] [DOI] [Wikipedia: Nuciferine] [Download PDF]
McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes. ACS Chem Biol. 2016 Apr 15; 11(4):992-1000. [PubMed] [DOI] [Download PDF]
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. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem. 2016 Feb 25; 59(4):1580-98. [PubMed] [DOI] [Practical Fragements] [UCSF Pharmacy - Recent Research] [Download PDF]
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. The promise and peril of chemical probes. Nat Chem Biol. 2015 Aug; 11(8):536-41. [PubMed] [DOI]
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. Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. Nature. 2015 Nov 26; 527(7579):477-83. [PubMed] [DOI] [ACS Chem. Biol. Spotlight] [Download PDF]
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. Corrigendum: The promise and peril of chemical probes. Nat Chem Biol. 2015 Nov; 11(11):887. [PubMed] [DOI] [Download PDF]
Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 2015 Oct 22; 58(20):8285-8291. [PubMed] [DOI] [Download PDF]
Barelier S, Sterling T, O'Meara MJ, Shoichet BK. The Recognition of Identical Ligands by Unrelated Proteins. ACS Chem Biol. 2015 Dec 18; 10(12):2772-84. [PubMed] [DOI] [In the Pipeline] [The Curious Wavefunction] [Download PDF]
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. Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference. ACS Chem Biol. 2015 Nov 20; 10(11):2616-23. [PubMed] [DOI] [Download PDF]
Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM. Prediction and validation of enzyme and transporter off-targets for metformin. J Pharmacokinet Pharmacodyn. 2015 Oct; 42(5):463-75. [PubMed] [DOI] [Download PDF]
Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK. An Aggregation Advisor for Ligand Discovery. J Med Chem. 2015 Sep 10; 58(17):7076-87. [PubMed] [DOI] [In The Pipeline] [Download PDF]
Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL. Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents. ACS Chem Biol. 2015 Oct 16; 10(10):2209-18. [PubMed] [DOI] [Download PDF]
Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem. 2015 Jul 27; 16(11):1560-4. [PubMed] [DOI] [Download PDF]
Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Homologous ligands accommodated by discrete conformations of a buried cavity. Proc Natl Acad Sci U S A. 2015 Apr 21; 112(16):5039-44. [PubMed] [DOI] [Download PDF]
London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2015 Mar; 11(3):235. [PubMed] [DOI] [Download PDF]
Duan D, Doak AK, Nedyalkova L, Shoichet BK. Colloidal aggregation and the in vitro activity of traditional Chinese medicines. ACS Chem Biol. 2015 Apr 17; 10(4):978-88. [PubMed] [DOI] [Faculty of 1000] [Download PDF]
London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 2015 Jan 20; 54(2):528-37. [PubMed] [DOI] [Download PDF]
Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP. Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative. J Med Chem. 2014 Jun 26; 57(12):5449-58. [PubMed] [DOI] [Download PDF]
London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Dec; 10(12):1066-72. [PubMed] [DOI] [Download PDF]
Avasthi P, Onishi M, Karpiak J, Yamamoto R, Mackinder L, Jonikas MC, Sale WS, Shoichet B, Pringle JR, Marshall WF. Actin is required for IFT regulation in Chlamydomonas reinhardtii. Curr Biol. 2014 Sep 08; 24(17):2025-32. [PubMed] [DOI] [Download PDF]
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. Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. Biochemistry. 2014 Jul 22; 53(28):4727-38. [PubMed] [DOI] [Download PDF]
Fischer M, Coleman RG, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem. 2014 Jul; 6(7):575-83. [PubMed] [DOI] [Download PDF]
Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol. 2014 Jul 18; 9(7):1528-35. [PubMed] [DOI] [Practical Fragments Blog] [Download PDF]
Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. [PubMed] [DOI] [Download PDF]
Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK. Substrate deconstruction and the nonadditivity of enzyme recognition. J Am Chem Soc. 2014 May 21; 136(20):7374-82. [PubMed] [DOI] [Chem & Eng NEWS] [Download PDF]
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. Large-scale identification and analysis of suppressive drug interactions. Chem Biol. 2014 Apr 24; 21(4):541-551. [PubMed] [DOI] [Download PDF]
Shoichet BK. Drug discovery: follow your lead. Nat Chem Biol. 2014 Apr; 10(4):244-5. [PubMed] [DOI] [Download PDF]
Owen SC, Doak AK, Ganesh AN, Nedyalkova L, McLaughlin CK, Shoichet BK, Shoichet MS. Colloidal drug formulations can explain "bell-shaped" concentration-response curves. ACS Chem Biol. 2014 Mar 21; 9(3):777-84. [PubMed] [DOI] [Download PDF]
Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol. 2013 May 17; 8(5):1018-26. [PubMed] [DOI] [Download PDF]
Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K. In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol. 2013 Nov; 11(11):e1001712. [PubMed] [DOI] [Download PDF]
Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One. 2013; 8(10):e75992. [PubMed] [DOI] [Download PDF]
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. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17; 52(37):6525-36. [PubMed] [DOI] [Download PDF]
Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. Structure-guided discovery of new deaminase enzymes. J Am Chem Soc. 2013 Sep 18; 135(37):13927-33. [PubMed] [DOI] [Download PDF]
Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol. 2013 Nov 15; 425(22):4569-83. [PubMed] [DOI] [F1000 Prime Recommended] [Download PDF]
Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK. Muscarinic receptors as model targets and antitargets for structure-based ligand discovery. Mol Pharmacol. 2013 Oct; 84(4):528-40. [PubMed] [DOI] [Download PDF]
Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities. PLoS One. 2013; 8(7):e69153. [PubMed] [DOI] [Download PDF]
Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ. Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem. 2013 Jul 05; 288(27):19830-44. [PubMed] [DOI] [Download PDF]
Merski M, Shoichet BK. The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. J Med Chem. 2013 Apr 11; 56(7):2874-84. [PubMed] [DOI] [Download PDF]
Sassano MF, Doak AK, Roth BL, Shoichet BK. Colloidal aggregation causes inhibition of G protein-coupled receptors. J Med Chem. 2013 Mar 28; 56(6):2406-14. [PubMed] [DOI] [Download PDF]
Cameron RT, Coleman RG, Day JP, Yalla KC, Houslay MD, Adams DR, Shoichet BK, Baillie GS. Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). Biochem Pharmacol. 2013 May 01; 85(9):1297-305. [PubMed] [DOI] [Download PDF]
Lin H, Sassano MF, Roth BL, Shoichet BK. A pharmacological organization of G protein-coupled receptors. Nat Methods. 2013 Feb; 10(2):140-6. [PubMed] [DOI] [Download PDF]
Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc. 2013 Jan 16; 135(2):795-803. [PubMed] [DOI] [Download PDF]
Shoichet BK. Drug discovery: nature's pieces. Nat Chem. 2013 Jan; 5(1):9-10. [PubMed] [DOI] [Download PDF]
Ornelas A, Korczynska M, Ragumani S, Kumaran D, Narindoshvili T, Shoichet BK, Swaminathan S, Raushel FM. Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily. Biochemistry. 2013 Jan 08; 52(1):228-38. [PubMed] [DOI] [Download PDF]
Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F. Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo. Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17448-53. [PubMed] [DOI] [Download PDF]
Merski M, Shoichet BK. Engineering a model protein cavity to catalyze the Kemp elimination. Proc Natl Acad Sci U S A. 2012 Oct 02; 109(40):16179-83. [PubMed] [DOI] [Download PDF]
Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem. 2012 Jul 26; 55(14):6582-94. [PubMed] [DOI] [Download PDF]
Gregori-Puigjané E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK. Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A. 2012 Jul 10; 109(28):11178-83. [PubMed] [DOI] [Download PDF]
Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L. Large-scale prediction and testing of drug activity on side-effect targets. Nature. 2012 Jun 10; 486(7403):361-7. [PubMed] [DOI] [Advance ePub] [ChEMBL Blog] [Science Daily] [UCSF Press Release] [Download PDF]
Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK. Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. ACS Chem Biol. 2012 Aug 17; 7(8):1429-35. [PubMed] [DOI] [In The Pipeline] [The Curious Wavefunction] [Download PDF]
John J. Irwin, Teague Sterling, Michael M. Mysinger, Erin S. Bolstad, and Ryan G. Coleman. ZINC: A Free Tool to Discover Chemistry for Biology. J. Chem. Inf. Model. 2012 52 (7), 1757-1768 [PubMed] [DOI] [Download PDF]
Shoichet BK, Kobilka BK. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci. 2012 May; 33(5):268-72. [PubMed] [DOI] [Download PDF]
Mysinger MM, Weiss DR, Ziarek JJ, Gravel S, Doak AK, Karpiak J, Heveker N, Shoichet BK, Volkman BF. Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5517-22. [PubMed] [DOI] [Download PDF]
Avasthi P, Marley A, Lin H, Gregori-Puigjane E, Shoichet BK, von Zastrow M, Marshall WF. A chemical screen identifies class a g-protein coupled receptors as regulators of cilia. ACS Chem Biol. 2012 May 18; 7(5):911-9. [PubMed] [DOI] [Download PDF]
Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry. 2012 Feb 28; 51(8):1762-73. [PubMed] [DOI] [Download PDF]
Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK. Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol. 2011 Dec 18; 8(2):144-6. [PubMed] [DOI] [Download PDF]
Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92. [PubMed] [DOI] [Download PDF]
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. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. [PubMed] [DOI] [Download PDF]
Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Sep 18; 7(11):769-78. [PubMed] [DOI] [F1000 Evaluation] [NRDD Highlight] [Download PDF]
Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A. Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A. 2011 Sep 20; 108(38):15810-5. [PubMed] [DOI] [Download PDF]
Poncet-Montange G, St Martin SJ, Bogatova OV, Prusiner SB, Shoichet BK, Ghaemmaghami S. A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets. J Biol Chem. 2011 Aug 05; 286(31):27718-28. [PubMed] [DOI] [JBC Full Text] [Download PDF]
Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 2011 Feb 23; 133(7):2080-3. [PubMed] [DOI] [Download PDF]
Eidam O, Romagnoli C, Caselli E, Babaoglu K, Pohlhaus DT, Karpiak J, Bonnet R, Shoichet BK, Prati F. Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as β-lactamase inhibitors. J Med Chem. 2010 Nov 11; 53(21):7852-63. [PubMed] [DOI] [Download PDF]
Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry. 2010 Dec 07; 49(48):10267-76. [PubMed] [DOI] [Download PDF]
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. The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology. 2011 Feb; 36(3):638-51. [PubMed] [DOI] [Download PDF]
Mysinger MM, Shoichet BK. Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model. 2010 Sep 27; 50(9):1561-73. [PubMed] [DOI] [Download PDF]
Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem. 2010 Jul 08; 53(13):4891-905. [PubMed] [DOI] [Download PDF]
Doak AK, Wille H, Prusiner SB, Shoichet BK. Colloid formation by drugs in simulated intestinal fluid. J Med Chem. 2010 May 27; 53(10):4259-65. [PubMed] [DOI] [Download PDF]
Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA. Structure-based discovery of A2A adenosine receptor ligands. J Med Chem. 2010 May 13; 53(9):3748-55. [PubMed] [DOI] [Download PDF]
Tondi D, Calò S, Shoichet BK, Costi MP. Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors. Bioorg Med Chem Lett. 2010 Jun 01; 20(11):3416-9. [PubMed] [DOI] [Download PDF]
DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD. Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs. J Med Chem. 2010 Mar 25; 53(6):2464-71. [PubMed] [DOI] [Download PDF]
Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 2010 Feb 17; 132(6):1762-3. [PubMed] [DOI] [Download PDF]
Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM. Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase . Biochemistry. 2010 Jan 26; 49(3):611-22. [PubMed] [DOI] [Download PDF]
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. Rapid behavior-based identification of neuroactive small molecules in the zebrafish. Nat Chem Biol. 2010 Mar; 6(3):231-237. [PubMed] [DOI] [Download PDF]
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. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem. 2010 Jan 14; 53(1):52-60. [PubMed] [DOI] [Download PDF]
Jadhav A, Ferreira RS, Klumpp C, Mott BT, Austin CP, Inglese J, Thomas CJ, Maloney DJ, Shoichet BK, Simeonov A. Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem. 2010 Jan 14; 53(1):37-51. [PubMed] [DOI] [Download PDF]
Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol. 2010 Feb 12; 396(1):47-59. [PubMed] [DOI] [Download PDF]
Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. Molecular docking screens using comparative models of proteins. J Chem Inf Model. 2009 Nov; 49(11):2512-27. [PubMed] [DOI] [Download PDF]
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. Predicting new molecular targets for known drugs. Nature. 2009 Nov 12; 462(7270):175-81. [PubMed] [DOI] [Download PDF]
Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK. Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc. 2009 Oct 14; 131(40):14345-54. [PubMed] [DOI] [ACS Chemical Biology Spotlight] [C&EN Article] [Faculty of 1000 Biology Comments] [Nature Chemistry research highlight] [Nature News & Views] [Wired article] [Download PDF]
Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y. Automated docking screens: a feasibility study. J Med Chem. 2009 Sep 24; 52(18):5712-20. [PubMed] [DOI] [Download PDF]
Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol. 2009 Dec 11; 394(4):747-63. [PubMed] [DOI] [Download PDF]
Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol. 2009 Aug; 20(4):429-36. [PubMed] [DOI] [Download PDF]
Ferreira RS, Bryant C, Ang KK, McKerrow JH, Shoichet BK, Renslo AR. Divergent modes of enzyme inhibition in a homologous structure-activity series. J Med Chem. 2009 Aug 27; 52(16):5005-8. [PubMed] [DOI] [Download PDF]
Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. Quantifying biogenic bias in screening libraries. Nat Chem Biol. 2009 Jul; 5(7):479-83. [PubMed] [DOI] [Biotechniques article] [Chemical & Engineering News article] [Chemistry World article] [In the Pipeline article] [The Curious Wavefunction article] [Download PDF]
Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK. Docking for fragment inhibitors of AmpC beta-lactamase. Proc Natl Acad Sci U S A. 2009 May 05; 106(18):7455-60. [PubMed] [DOI] [Download PDF]
Coan KE, Maltby DA, Burlingame AL, Shoichet BK. Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem. 2009 Apr 09; 52(7):2067-75. [PubMed] [DOI] [Faculty of 1000] [Download PDF]
Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK. Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6843-8. [PubMed] [DOI] [Download PDF]
Chen Y, Shoichet BK. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol. 2009 May; 5(5):358-64. [PubMed] [DOI] [News and Views] [Download PDF]
Xiang DF, Kolb P, Fedorov AA, Meier MM, Fedorov LV, Nguyen TT, Sterner R, Almo SC, Shoichet BK, Raushel FM. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry. 2009 Mar 17; 48(10):2237-47. [PubMed] [DOI] [Download PDF]
Chen Y, McReynolds A, Shoichet BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Sci. 2009 Mar; 18(3):662-9. [PubMed] [DOI] [Download PDF]
Marciano DC, Pennington JM, Wang X, Wang J, Chen Y, Thomas VL, Shoichet BK, Palzkill T. Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase. J Mol Biol. 2008 Dec 05; 384(1):151-64. [PubMed] [DOI] [Download PDF]
Huang N, Shoichet BK. Exploiting ordered waters in molecular docking. J Med Chem. 2008 Aug 28; 51(16):4862-5. [PubMed] [DOI] [Download PDF]
Coan KE, Shoichet BK. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc. 2008 Jul 23; 130(29):9606-12. [PubMed] [DOI] [Download PDF]
Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. Quantifying the relationships among drug classes. J Chem Inf Model. 2008 Apr; 48(4):755-65. [PubMed] [DOI] [Download PDF]
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. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem. 2008 Apr 24; 51(8):2502-11. [PubMed] [DOI] [Download PDF]
Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol. 2008 Mar 28; 377(3):914-34. [PubMed] [DOI] [Download PDF]
Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol. 2008 Mar; 4(3):197-9. [PubMed] [DOI] [Nature Chem. Bio. Five years in review] [Download PDF]
Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F. Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorg Med Chem. 2008 Feb 01; 16(3):1195-205. [PubMed] [DOI] [Download PDF]
Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G, Shoichet BK, Costi MP. Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy. J Med Chem. 2007 Nov 15; 50(23):5644-54. [PubMed] [DOI] [Download PDF]
Delmas J, Chen Y, Prati F, Robin F, Shoichet BK, Bonnet R. Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol. 2008 Jan 04; 375(1):192-201. [PubMed] [DOI] [Download PDF]
Shoichet BK. No free energy lunch. Nat Biotechnol. 2007 Oct; 25(10):1109-10. [PubMed] [DOI] [Download PDF]
Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF. O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site. J Am Chem Soc. 2007 Aug 08; 129(31):9548-9. [PubMed] [DOI] [Download PDF]
Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. Nature. 2007 Aug 16; 448(7155):775-9. [PubMed] [DOI] [Download PDF]
Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 2007 Aug 24; 371(4):1118-34. [PubMed] [DOI] [Download PDF]
Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 2007 Jun 12; 46(23):6688-95. [PubMed] [DOI] [Download PDF]
Feng BY, Simeonov A, Jadhav A, Babaoglu K, Inglese J, Shoichet BK, Austin CP. A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem. 2007 May 17; 50(10):2385-90. [PubMed] [DOI] [Download PDF]
Chen Y, Bonnet R, Shoichet BK. The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution. J Am Chem Soc. 2007 May 02; 129(17):5378-80. [PubMed] [DOI] [Download PDF]
Shoichet B. An interview with Brian Shoichet, Ph.D. Professor, Department of Pharmaceutical Chemistry, University of California, San Francisco. Assay Drug Dev Technol. 2007 Apr; 5(2):157-61. [PubMed] [DOI] [Article]
Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007 Feb; 25(2):197-206. [PubMed] [DOI] [Download PDF]
Coan KE, Shoichet BK. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst. 2007 Mar; 3(3):208-13. [PubMed] [DOI] [Download PDF]
Shoichet BK. Interpreting steep dose-response curves in early inhibitor discovery. J Med Chem. 2006 Dec 14; 49(25):7274-7. [PubMed] [DOI] [Download PDF]
Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc. 2006 Dec 13; 128(49):15882-91. [PubMed] [DOI] [Download PDF]
Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM. Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library. J Am Chem Soc. 2006 Dec 13; 128(49):15892-902. [PubMed] [DOI] [Download PDF]
Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801. [PubMed] [DOI] [Download PDF]
Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nat Chem Biol. 2006 Dec; 2(12):720-3. [PubMed] [DOI] [Download PDF]
Leach AR, Shoichet BK, Peishoff CE. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem. 2006 Oct 05; 49(20):5851-5. [PubMed] [DOI] [Download PDF]
Shoichet BK. Screening in a spirit haunted world. Drug Discov Today. 2006 Jul; 11(13-14):607-15. [PubMed] [DOI] [Download PDF]
Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem. 2006 Apr 06; 49(7):2151-4. [PubMed] [DOI] [Download PDF]
Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc. 2006 Mar 08; 128(9):2970-6. [PubMed] [DOI] [Download PDF]
Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK. Probing molecular docking in a charged model binding site. J Mol Biol. 2006 Apr 14; 357(5):1449-70. [PubMed] [DOI] [Download PDF]
Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nat Protoc. 2006; 1(2):550-3. [PubMed] [DOI] [Download PDF]
Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 2005 Sep 20; 44(37):12316-28. [PubMed] [DOI] [Download PDF]
Brenk R, Irwin JJ, Shoichet BK. Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen. 2005 Oct; 10(7):667-74. [PubMed] [DOI] [Download PDF]
Thomas VL, Golemi-Kotra D, Kim C, Vakulenko SB, Mobashery S, Shoichet BK. Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry. 2005 Jul 05; 44(26):9330-8. [PubMed] [DOI] [Download PDF]
Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK. High-throughput assays for promiscuous inhibitors. Nat Chem Biol. 2005 Aug; 1(3):146-8. [PubMed] [DOI] [Download PDF]
Graves AP, Brenk R, Shoichet BK. Decoys for docking. J Med Chem. 2005 Jun 02; 48(11):3714-28. [PubMed] [DOI] [PDB 1XEP] [Download PDF]
Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R. Atomic resolution structures of CTX-M beta-lactamases: extended spectrum activities from increased mobility and decreased stability. J Mol Biol. 2005 Apr 29; 348(2):349-62. [PubMed] [DOI] [PDB 1YLJ] [PDB 1YLP] [PDB 1YLT] [PDB 1YLW] [Download PDF]
Chen Y, Shoichet B, Bonnet R. Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases. J Am Chem Soc. 2005 Apr 20; 127(15):5423-34. [PubMed] [DOI] [Download PDF]
Tondi D, Morandi F, Bonnet R, Costi MP, Shoichet BK. Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture. J Am Chem Soc. 2005 Apr 06; 127(13):4632-9. [PubMed] [DOI] [PDB 1XGI] [PDB 1XGJ] [Download PDF]
Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem. 2005; 5(8):739-49. [PubMed] [DOI] [Download PDF]
Irwin JJ, Shoichet BK. ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005 Jan-Feb; 45(1):177-82. [PubMed] [DOI] [Supporting Info] [Download PDF]
Shoichet BK. Virtual screening of chemical libraries. Nature. 2004 Dec 16; 432(7019):862-5. [PubMed] [DOI] [Download PDF]
Ferrari AM, Wei BQ, Costantino L, Shoichet BK. Soft docking and multiple receptor conformations in virtual screening. J Med Chem. 2004 Oct 07; 47(21):5076-84. [PubMed] [DOI] [Download PDF]
Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol. 2004 Apr 09; 337(5):1161-82. [PubMed] [DOI] [PDB 1OV5] [PDB 1OV7] [PDB 1OVH] [PDB 1OVJ] [PDB 1OVK] [PDB 1OWY] [PDB 1OWZ] [Supplementary Material] [Download PDF]
Horn JR, Shoichet BK. Allosteric inhibition through core disruption. J Mol Biol. 2004 Mar 05; 336(5):1283-91. [PubMed] [DOI] [PDB 1PZO] [PDB 1PZP] [Download PDF]
Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK. Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Biochemistry. 2003 Dec 16; 42(49):14483-91. [PubMed] [DOI] [Download PDF]
Seidler J, McGovern SL, Doman TN, Shoichet BK. Identification and prediction of promiscuous aggregating inhibitors among known drugs. J Med Chem. 2003 Oct 09; 46(21):4477-86. [PubMed] [DOI] [Supporting Info] [newsinbrief] [Download PDF]
McGovern SL, Helfand BT, Feng B, Shoichet BK. A specific mechanism of nonspecific inhibition. J Med Chem. 2003 Sep 25; 46(20):4265-72. [PubMed] [DOI] [Download PDF]
Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S. Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. J Am Chem Soc. 2003 Aug 13; 125(32):9612-8. [PubMed] [DOI] [Download PDF]
Wang X, Minasov G, Blázquez J, Caselli E, Prati F, Shoichet BK. Recognition and resistance in TEM beta-lactamase. Biochemistry. 2003 Jul 22; 42(28):8434-44. [PubMed] [DOI] [Download PDF]
McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem. 2003 Jul 03; 46(14):2895-907. [PubMed] [DOI] [Supporting Info] [Download PDF]
McGovern SL, Shoichet BK. Kinase inhibitors: not just for kinases anymore. J Med Chem. 2003 Apr 10; 46(8):1478-83. [PubMed] [DOI] [Faculty of 1000] [In Brief] [Download PDF]
Soelaiman S, Wei BQ, Bergson P, Lee YS, Shen Y, Mrksich M, Shoichet BK, Tang WJ. Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J Biol Chem. 2003 Jul 11; 278(28):25990-7. [PubMed] [DOI] [Download PDF]
Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS. A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase. J Biol Chem. 2003 Apr 18; 278(16):14092-100. [PubMed] [DOI] [Faculty of 1000] [Download PDF]
Morandi F, Caselli E, Morandi S, Focia PJ, Blázquez J, Shoichet BK, Prati F. Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc. 2003 Jan 22; 125(3):685-95. [PubMed] [DOI] [News In Brief] [PDB 1MXO] [PDB 1MY8] [Download PDF]
Beadle BM, Shoichet BK. Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother. 2002 Dec; 46(12):3978-80. [PubMed] [DOI] [PDB 1LL5] [Download PDF]
Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK. A model binding site for testing scoring functions in molecular docking. J Mol Biol. 2002 Sep 13; 322(2):339-55. [PubMed] [DOI] [PDB 1LGU] [PDB 1LGW] [PDB 1LGX] [PDB 1LI2] [PDB 1LI3] [PDB 1LI6] [Download PDF]
Trehan I, Morandi F, Blaszczak LC, Shoichet BK. Using steric hindrance to design new inhibitors of class C beta-lactamases. Chem Biol. 2002 Sep; 9(9):971-80. [PubMed] [DOI] [PDB 1LL9] [PDB 1LLB] [Download PDF]
Beadle BM, Shoichet BK. Structural bases of stability-function tradeoffs in enzymes. J Mol Biol. 2002 Aug 09; 321(2):285-96. [PubMed] [DOI] [PDB 1L0D] [PDB 1L0E] [PDB 1L0F] [PDB 1L0G] [Download PDF]
Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking. Curr Opin Chem Biol. 2002 Aug; 6(4):439-46. [PubMed] [DOI] [Download PDF]
Powers RA, Shoichet BK. Structure-based approach for binding site identification on AmpC beta-lactamase. J Med Chem. 2002 Jul 18; 45(15):3222-34. [PubMed] [DOI] [PDB 1KDS] [PDB 1KDW] [PDB 1KE0] [PDB 1KE3] [PDB 1KE4] [Supporting Info] [Download PDF]
Powers RA, Morandi F, Shoichet BK. Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure. 2002 Jul; 10(7):1013-23. [PubMed] [DOI] [PDB 1L2S] [Download PDF]
Wang X, Minasov G, Shoichet BK. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol. 2002 Jun 28; 320(1):85-95. [PubMed] [DOI] [PDB 1LHY] [PDB 1LI0] [PDB 1LI9] [Download PDF]
Wang X, Minasov G, Shoichet BK. The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem. 2002 Aug 30; 277(35):32149-56. [PubMed] [DOI] [PDB 1JWP] [PDB 1JWV] [PDB 1JWZ] [Download PDF]
Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci. 2002 Jun; 11(6):1393-408. [PubMed] [DOI] [Download PDF]
Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem. 2002 May 23; 45(11):2213-21. [PubMed] [DOI] [Faculty of 1000] [NRDD Highlight] [Download PDF]
Minasov G, Wang X, Shoichet BK. An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc. 2002 May 15; 124(19):5333-40. [PubMed] [DOI] [PDB 1M40] [Download PDF]
McGovern SL, Caselli E, Grigorieff N, Shoichet BK. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem. 2002 Apr 11; 45(8):1712-22. [PubMed] [DOI] [C & EN News of the Week] [ESI Special Topics] [NRDD Highlight] [Download PDF]
Wang X, Minasov G, Shoichet BK. Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams. Proteins. 2002 Apr 01; 47(1):86-96. [PubMed] [PDB 1JVJ]
Beadle BM, Trehan I, Focia PJ, Shoichet BK. Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Structure. 2002 Mar; 10(3):413-24. [PubMed] [DOI] [Erratum] [Download PDF]
Powers RA, Caselli E, Focia PJ, Prati F, Shoichet BK. Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design. Biochemistry. 2001 Aug 07; 40(31):9207-14. [PubMed] [DOI] [PDB 1IEL] [PDB 1IEM] [Download PDF]
Trehan I, Beadle BM, Shoichet BK. Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site. Biochemistry. 2001 Jul 10; 40(27):7992-9. [PubMed] [DOI] [PDB 1I5Q] [Download PDF]
Beadle BM, Nicholas RA, Shoichet BK. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation. Protein Sci. 2001 Jun; 10(6):1254-9. [PubMed] [DOI] [Download PDF]
Tondi D, Powers RA, Caselli E, Negri MC, Blázquez J, Costi MP, Shoichet BK. Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase. Chem Biol. 2001 Jun; 8(6):593-611. [PubMed] [DOI] [PDB 1GA9] [Download PDF]
Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins. 2001 Feb 01; 42(2):279-93. [PubMed] [DOI]
Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK. Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases. Chem Biol. 2001 Jan; 8(1):17-31. [PubMed] [DOI] [PDB 1FSW] [PDB 1FSY] [Download PDF]
Patera A, Blaszczak LC, Shoichet BK. Crystal structures of substrate and inhibitor complexes with AmpC β-lactamase: possible implications for substrate-assisted catalysis. J Am Chem Soc 122 (43), 10504-12 (2000). [DOI] [PDB 1FCM] [PDB 1FCN] [PDB 1FCO] [Download PDF]
Shoichet BK, Bussiere DE. Macromolecular crystallography and lead discovery: possibilities and limitations (Review). Current Opinion in Drug Discovery & Development 3, 408-22 (2000).
Powers RA, Blázquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK. The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase. Protein Sci. 1999 Nov; 8(11):2330-7. [PubMed] [DOI] [Download PDF]
Beadle BM, McGovern SL, Patera A, Shoichet BK. Functional analyses of AmpC beta-lactamase through differential stability. Protein Sci. 1999 Sep; 8(9):1816-24. [PubMed] [DOI]
Tondi D, Slomczynska U, Costi MP, Watterson DM, Ghelli S, Shoichet BK. Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase. Chem Biol. 1999 May; 6(5):319-31. [PubMed] [DOI] [Download PDF]
Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry. 1999 Feb 23; 38(8):2570-6. [PubMed] [DOI] [Download PDF]
Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP. Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry. 1999 Feb 02; 38(5):1607-17. [PubMed] [DOI] [PDB 1TSL] [Download PDF]
Shoichet BK, Leach AR, Kuntz ID. Ligand solvation in molecular docking. Proteins. 1999 Jan 01; 34(1):4-16. [PubMed] [DOI]
Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ. Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design. Biochemistry. 1998 Nov 17; 37(46):16082-92. [PubMed] [DOI] [PDB 2BLS] [Download PDF]
Weston GS, Blázquez J, Baquero F, Shoichet BK. Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase. J Med Chem. 1998 Nov 05; 41(23):4577-86. [PubMed] [DOI] [Download PDF]
Morosini MI, Negri MC, Shoichet B, Baquero MR, Baquero F, Blázquez J. An extended-spectrum AmpC-type beta-lactamase obtained by in vitro antibiotic selection. FEMS Microbiol Lett. 1998 Aug 01; 165(1):85-90. [PubMed] [DOI] [Download PDF]
Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Sci. 1998 Apr; 7(4):938-50. [PubMed] [DOI] [Download PDF]
Shoichet BK. Receptor Preorganization for Activity and its Role in Identifying Ligand-Binding Sites on Proteins. In Practical Application of Computer-Aided Drug Design (ed. Charifson PS), pp. 195-226 (Marcel Dekker Inc, New York, 1997).
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. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol. 1996 Mar; 3(3):233-9. [PubMed] [DOI]
Shoichet BK. Docking ligands to proteins. In Protein Structure Prediction A Practical Approach (ed. Sternberg M.L.), pp. 263-290 (Oxford Press, 1996). [Download PDF]
Shoichet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction. Chem Biol. 1996 Mar; 3(3):151-6. [PubMed] [DOI] [Download PDF]
Zhang XJ, Baase WA, Shoichet BK, Wilson KP, Matthews BW. Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive. Protein Eng. 1995 Oct; 8(10):1017-22. [PubMed] [DOI]
Shoichet BK, Baase WA, Kuroki R, Matthews BW. A relationship between protein stability and protein function. Proc Natl Acad Sci U S A. 1995 Jan 17; 92(2):452-6. [PubMed] [DOI] [PDB 253L] [PDB 254L] [PDB 255L] [Download PDF]
Schellenberger U, Balaram P, Francis VS, Shoichet BK, Santi DV. Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion. Biochemistry. 1994 May 10; 33(18):5623-9. [PubMed] [DOI]
Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design. Accounts of Chemical Research 27, 117-123 (1994). [DOI] [Download PDF]
Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Eng. 1993 Sep; 6(7):723-32. [PubMed] [DOI]
Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science. 1993 Mar 05; 259(5100):1445-50. [PubMed] [DOI] [Download PDF]
Shoichet BK, Kuntz ID. Protein docking and complementarity. J Mol Biol. 1991 Sep 05; 221(1):327-46. [PubMed] [DOI]
Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P. Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis. Protein Eng. 1989 Nov; 3(2):95-103. [PubMed] [DOI] [Download PDF]