Lab Publications

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2021

• 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]

2020

• Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24. [PubMed]
• Irwin JJ, Tang KG, Young J, Dandarchuluun C, Wong BR, Khurelbaatar M, Moroz YS, Mayfield J, Sayle RA. ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J Chem Inf Model. 2020 Dec 28; 60(12):6065-6073. [PubMed]
• 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]
• Grant Glatfelter, Reed Stein, Hye Jin Kang, Anthony Jones, John Irwin, Bryan Roth, Brian Shoichet, Margarita Dubocovich. In vivo Efficacy of Novel Type Preferring MT1 Melatonin Receptor Inverse Agonists in C3H/HeN Mouse Models of Chronobiological Behavior. The FASEB Journal. 2020 Apr 1; 34(S1):1-1.
• 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 03 18; 142(11):4960-4964. [PubMed]
• 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 03; 579(7800):609-614. [PubMed]
• Ballante F, Rudling A, Zeifman A, Luttens A, Vo DD, Irwin JJ, Kihlberg J, Brea J, Loza MI, Carlsson J. Docking Finds GPCR Ligands in Dark Chemical Matter. J Med Chem. 2020 01 23; 63(2):613-620. [PubMed]

2019

• Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ. Ultra-large library docking for discovering new chemotypes. Nature. 2019 02; 566(7743):224-229. [PubMed]

2017

• Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ. Predicted Biological Activity of Purchasable Chemical Space. J Chem Inf Model. 2018 01 22; 58(1):148-164. [PubMed]
• 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]

2016

• Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One. 2016; 11(8):e0160365. [PubMed]
• Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 05 12; 59(9):4103-20. [PubMed]

2015

• ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015 Nov 23; 55(11):2324-37. [PubMed]
• An Aggregation Advisor for Ligand Discovery. J Med Chem. 2015 Sep 10; 58(17):7076-87. [PubMed]
• Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2015 Mar; 11(3):235. [PubMed]

2014

• Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Dec; 10(12):1066-72. [PubMed]
• Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol. 2014 Jul 18; 9(7):1528-35. [PubMed]
• Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells. Bioorg Med Chem. 2014 Mar 15; 22(6):1960-72. [PubMed]
• Nir London, Rand M. Miller, John J. Irwin, Oliv Eidam, Lucie Gibold, Richard Bonnet, Brian K. Shoichet, Jack Taunton. Covalent Docking of Large Libraries for the Discovery of Chemical Probes. Biophysical Journal. 2014 Jan 1; 106(2):264a.

2013

• Ligand pose and orientational sampling in molecular docking. PLoS One. 2013; 8(10):e75992. [PubMed]
• Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012. [PubMed]
• Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem. 2013 Jul 05; 288(27):19830-44. [PubMed]
• Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5480-5. [PubMed]

2012

• 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]
• Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A. 2012 Jul 10; 109(28):11178-83. [PubMed]
• ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012 Jul 23; 52(7):1757-68. [PubMed]
• Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26. [PubMed]

2011

• Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol. 2011 Dec 18; 8(2):144-6. [PubMed]
• Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92. [PubMed]
• Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Sep 18; 7(11):769-78. [PubMed]
• 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]

2010

• Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry. 2010 Dec 07; 49(48):10267-76. [PubMed]
• 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]
• 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]
• 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]
• Dennis R, Fox T, Fuentes M, Gilliland A, Hanna S, Hogrefe C, Irwin J, Rao ST, Scheffe R, Schere K, Steyn D, Venkatram A. A FRAMEWORK FOR EVALUATING REGIONAL-SCALE NUMERICAL PHOTOCHEMICAL MODELING SYSTEMS. Environ Fluid Mech (Dordr). 2010; 10(4):471-489. [PubMed]

2009

• 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]
• 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]
• 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]
• 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]
• Irwin JJ. Staring off into chemical space. Nat Chem Biol. 2009 Aug; 5(8):536-7. [PubMed]
• 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]
• 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]
• Kolb P, Irwin JJ. Docking screens: right for the right reasons? Curr Top Med Chem. 2009; 9(9):755-70. [PubMed]

2008

• Jerome Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet. ChemInform Abstract: Quantifying the Relationships among Drug Classes. ChemInform. 2008 Jul 15; 39(29).
• John S. Irwin, Kevin Civerolo, Christian Hogrefe, Wyat Appel, Kristen Foley, Jenise Swall. A procedure for inter-comparing the skill of regional-scale air quality model simulations of daily maximum 8-h ozone concentrations. Atmospheric Environment. 2008 Jul 1; 42(21):5403-5412.
• Irwin JJ. Using ZINC to acquire a virtual screening library. Curr Protoc Bioinformatics. 2008 Jun; Chapter 14:Unit 14.6. [PubMed]
• 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]
• 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]
• Irwin JJ. Community benchmarks for virtual screening. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):193-9. [PubMed]
• C. Hogrefe, J. -Y. Ku, G. Sistla, A. Gilliland, J. S. Irwin, P. S. Porter, E. Gégo, P. Kasibhatla, S. T. Rao. Has the Performance of Regional-Scale Photochemical Modelling Systems Changed over the Past Decade?. . 2008 Jan 1; 394-403.

2007

• Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M. Chemistry in cancer research: a vital partnership. Cancer Res. 2007 Jul 15; 67(14):6539-43. [PubMed]
• Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M. Chemistry in cancer research: a vital partnership. ACS Chem Biol. 2007 May 22; 2(5):286-92. [PubMed]
• 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]
• Christian Hogrefe, J. M. Jones, A. Gilliland, P. Steven Porter, Edith Gégo, R. Gilliam, J. Swall, J. Irwin, S. T. Rao. Evaluation of an Annual Simulation of Ozone and Fine Particulate Matter over the Continental United States – Which Temporal Features are Captured?. . 2007 Jan 1; 562-570.
• Edith Gégo, P. Steven Porter, Christian Hogrefe, R. Gilliam, A. Gilliland, J. Swall, J. Irwin, S. T. Rao. Objective Reduction of the Space-Time Domain Dimensionality for Evaluating Model Performance. . 2007 Jan 1; 543-552.
• P. S. Porter, J. Swall, R. Gillian, E. L. Gego, Christian Hogrefe, A. Gilliland, J. S. Irwin, T. Rao. Temporal Signatures of Observations and Model Outputs: Do Time Series Decomposition Methods Capture Relevant Time Scales?. . 2007 Jan 1; 421-429.

2006

• 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]
• Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801. [PubMed]
• Edith Gégo, P. Steven Porter, Christian Hogrefe, John S. Irwin. An objective comparison of CMAQ and REMSAD performances. Atmospheric Environment. 2006 Aug 1; 40(26):4920-4934.
• C. Hogrefe, P.S. Porter, E. Gego, A. Gilliland, R. Gilliam, J. Swall, J. Irwin, S.T. Rao. Temporal features in observed and simulated meteorology and air quality over the Eastern United States. Atmospheric Environment. 2006 Aug 1; 40(26):5041-5055.
• Irwin JJ. How good is your screening library? Curr Opin Chem Biol. 2006 Aug; 10(4):352-6. [PubMed]
• Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model. 2006 Jan-Feb; 46(1):243-53. [PubMed]

2005

• Edith L Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao. Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks. Pure and Applied Geophysics. 2005 Oct 1; 162(10):1919-1939.
• Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 2005 Sep 20; 44(37):12316-28. [PubMed]
• 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]
• John J. Irwin, Brian K. Shoichet. ZINC — A Free Database of Commercially Available Compounds for Virtual Screening. ChemInform. 2005 Apr 19; 36(16).
• Edith Gego, Christian Hogrefe, George Kallos, Antigoni Voudouri, John S. Irwin, S. Trivikrama Rao. Examination of model predictions at different horizontal grid resolutions. Environmental Fluid Mechanics. 2005 Apr 1; 5(1-2):63-85.
• Edith L. Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao. Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks. . 2005 Jan 1; 1919-1939.
• 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]

2004

• Edith L. Gego, Christian Hogrefe, P. Steven Porter, John S. Irwin, S. Trivikrama Rao. Comparison of the Space-Time Signatures of Air Quality Data From Different Monitoring Networks. . 2004 Jan 1; 481-490.

2003

• 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]

2002

• Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking. Curr Opin Chem Biol. 2002 Aug; 6(4):439-46. [PubMed]