John Irwin, PhD
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Title(s) | Adjunct Professor, Pharmaceutical Chemistry |
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School | School of Pharmacy |
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Address | 1700 4th St San Francisco CA 94158
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Phone | 415-878-1705 |
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ORCID
.gif) | 0000-0002-1195-6417  |
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vCard | Download vCard |
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Research ORNG Applications Bibliographic
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media.
(Note that publications are often cited in additional ways that are not shown here.)
Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication.
Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication.
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Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model. 2021 Jan 25.
Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. PMID: 33494610.
View in: PubMed Mentions: Fields:
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Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24.
PMID: 33269349.
View in: PubMed Mentions:
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ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J Chem Inf Model. 2020 Dec 28; 60(12):6065-6073.
Irwin JJ, Tang KG, Young J, Dandarchuluun C, Wong BR, Khurelbaatar M, Moroz YS, Mayfield J, Sayle RA. PMID: 33118813.
View in: PubMed Mentions: 1 Fields:
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The activities of drug inactive ingredients on biological targets. Science. 2020 07 24; 369(6502):403-413.
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. PMID: 32703874.
View in: PubMed Mentions: 1 Fields: Translation: HumansAnimals
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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.
Grant Glatfelter, Reed Stein, Hye Jin Kang, Anthony Jones, John Irwin, Bryan Roth, Brian Shoichet, Margarita Dubocovich. .
View in: Publisher Site Mentions:
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Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. J Am Chem Soc. 2020 03 18; 142(11):4960-4964.
Wan X, Yang T, Cuesta A, Pang X, Balius TE, Irwin JJ, Shoichet BK, Taunton J. PMID: 32105459.
View in: PubMed Mentions: 3 Fields:
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Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. 2020 03; 579(7800):609-614.
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. PMID: 32040955.
View in: PubMed Mentions: 8 Fields: Translation: HumansAnimals
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Docking Finds GPCR Ligands in Dark Chemical Matter. J Med Chem. 2020 01 23; 63(2):613-620.
Ballante F, Rudling A, Zeifman A, Luttens A, Vo DD, Irwin JJ, Kihlberg J, Brea J, Loza MI, Carlsson J. PMID: 31846328.
View in: PubMed Mentions: Fields: Translation: HumansCells
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Ultra-large library docking for discovering new chemotypes. Nature. 2019 02; 566(7743):224-229.
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. PMID: 30728502.
View in: PubMed Mentions: 42 Fields: Translation: Humans
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Predicted Biological Activity of Purchasable Chemical Space. J Chem Inf Model. 2018 01 22; 58(1):148-164.
Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ. PMID: 29193970.
View in: PubMed Mentions: 2 Fields:
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Discovery of new GPCR ligands to illuminate new biology. Nat Chem Biol. 2017 Nov; 13(11):1143-1151.
Roth BL, Irwin JJ, Shoichet BK. PMID: 29045379.
View in: PubMed Mentions: 16 Fields: Translation: HumansCells
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Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One. 2016; 11(8):e0160365.
PMID: 27490099.
View in: PubMed Mentions: 3 Fields: Translation: HumansAnimals
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Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 05 12; 59(9):4103-20.
PMID: 26913380.
View in: PubMed Mentions: 47 Fields:
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ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015 Nov 23; 55(11):2324-37.
PMID: 26479676.
View in: PubMed Mentions: 219 Fields: Translation: HumansAnimals
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An Aggregation Advisor for Ligand Discovery. J Med Chem. 2015 Sep 10; 58(17):7076-87.
PMID: 26295373.
View in: PubMed Mentions: 64 Fields:
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Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2015 Mar; 11(3):235.
PMID: 25689339.
View in: PubMed Mentions: Fields:
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Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Dec; 10(12):1066-72.
PMID: 25344815.
View in: PubMed Mentions: 39 Fields: Translation: HumansAnimalsCells
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Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol. 2014 Jul 18; 9(7):1528-35.
PMID: 24807704.
View in: PubMed Mentions: 10 Fields: Translation: Cells
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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.
PMID: 24530226.
View in: PubMed Mentions: 6 Fields: Translation: HumansAnimalsCells
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Covalent Docking of Large Libraries for the Discovery of Chemical Probes. Biophysical Journal. 2014 Jan 1; 106(2):264a.
Nir London, Rand M. Miller, John J. Irwin, Oliv Eidam, Lucie Gibold, Richard Bonnet, Brian K. Shoichet, Jack Taunton. .
View in: Publisher Site Mentions:
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Ligand pose and orientational sampling in molecular docking. PLoS One. 2013; 8(10):e75992.
PMID: 24098414.
View in: PubMed Mentions: 27 Fields: Translation: Cells
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Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012.
PMID: 24183589.
View in: PubMed Mentions: 4 Fields: Translation: AnimalsCells
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Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem. 2013 Jul 05; 288(27):19830-44.
PMID: 23667258.
View in: PubMed Mentions: 32 Fields: Translation: HumansCells
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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.
PMID: 23509259.
View in: PubMed Mentions: 52 Fields: Translation: HumansCells
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Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem. 2012 Jul 26; 55(14):6582-94.
PMID: 22716043.
View in: PubMed Mentions: 284 Fields: Translation: HumansCells
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Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A. 2012 Jul 10; 109(28):11178-83.
PMID: 22711801.
View in: PubMed Mentions: 44 Fields: Translation: Humans
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ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012 Jul 23; 52(7):1757-68.
PMID: 22587354.
View in: PubMed Mentions: 493 Fields:
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Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26.
PMID: 22183533.
View in: PubMed Mentions: 6 Fields: Translation: Cells
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Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol. 2011 Dec 18; 8(2):144-6.
PMID: 22179068.
View in: PubMed Mentions: 44 Fields: Translation: Animals
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Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92.
PMID: 22014038.
View in: PubMed Mentions: 15 Fields: Translation: HumansAnimalsCells
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Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Sep 18; 7(11):769-78.
PMID: 21926995.
View in: PubMed Mentions: 103 Fields: Translation: Cells
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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.
PMID: 21885739.
View in: PubMed Mentions: 50 Fields: Translation: HumansCells
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The chemical basis of pharmacology. Biochemistry. 2010 Dec 07; 49(48):10267-76.
Keiser MJ, Irwin JJ, Shoichet BK. PMID: 21058655.
View in: PubMed Mentions: 27 Fields: Translation: HumansAnimalsCells
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The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology. 2011 Feb; 36(3):638-51.
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. PMID: 21048700.
View in: PubMed Mentions: 35 Fields: Translation: AnimalsCells
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Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem. 2010 Jul 08; 53(13):4891-905.
Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK. PMID: 20540517.
View in: PubMed Mentions: 45 Fields: Translation: Humans
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Structure-based discovery of A2A adenosine receptor ligands. J Med Chem. 2010 May 13; 53(9):3748-55.
Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA. PMID: 20405927.
View in: PubMed Mentions: 69 Fields: Translation: HumansCells
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A FRAMEWORK FOR EVALUATING REGIONAL-SCALE NUMERICAL PHOTOCHEMICAL MODELING SYSTEMS. Environ Fluid Mech (Dordr). 2010; 10(4):471-489.
Dennis R, Fox T, Fuentes M, Gilliland A, Hanna S, Hogrefe C, Irwin J, Rao ST, Scheffe R, Schere K, Steyn D, Venkatram A. PMID: 21461126.
View in: PubMed Mentions:
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Molecular docking screens using comparative models of proteins. J Chem Inf Model. 2009 Nov; 49(11):2512-27.
Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. PMID: 19845314.
View in: PubMed Mentions: 51 Fields: Translation: Cells
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Predicting new molecular targets for known drugs. Nature. 2009 Nov 12; 462(7270):175-81.
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. PMID: 19881490.
View in: PubMed Mentions: 456 Fields: Translation: HumansAnimals
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Automated docking screens: a feasibility study. J Med Chem. 2009 Sep 24; 52(18):5712-20.
Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y. PMID: 19719084.
View in: PubMed Mentions: 72 Fields: Translation: Cells
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Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol. 2009 Aug; 20(4):429-36.
Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. PMID: 19733475.
View in: PubMed Mentions: 51 Fields: Translation: Cells
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Staring off into chemical space. Nat Chem Biol. 2009 Aug; 5(8):536-7.
Irwin JJ. PMID: 19620992.
View in: PubMed Mentions: 1 Fields:
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Quantifying biogenic bias in screening libraries. Nat Chem Biol. 2009 Jul; 5(7):479-83.
Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. PMID: 19483698.
View in: PubMed Mentions: 51 Fields: Translation: Cells
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Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A. 2009 Apr 21; 106(16):6843-8.
Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK. PMID: 19342484.
View in: PubMed Mentions: 98 Fields: Translation: Cells
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Docking screens: right for the right reasons? Curr Top Med Chem. 2009; 9(9):755-70.
Kolb P, Irwin JJ. PMID: 19754393.
View in: PubMed Mentions: 20 Fields: Translation: Cells
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ChemInform Abstract: Quantifying the Relationships among Drug Classes. ChemInform. 2008 Jul 15; 39(29).
Jerome Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet. .
View in: Publisher Site Mentions:
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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.
John S. Irwin, Kevin Civerolo, Christian Hogrefe, Wyat Appel, Kristen Foley, Jenise Swall. .
View in: Publisher Site Mentions:
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Using ZINC to acquire a virtual screening library. Curr Protoc Bioinformatics. 2008 Jun; Chapter 14:Unit 14.6.
Irwin JJ. PMID: 18551414.
View in: PubMed Mentions: 6 Fields:
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Quantifying the relationships among drug classes. J Chem Inf Model. 2008 Apr; 48(4):755-65.
Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. PMID: 18335977.
View in: PubMed Mentions: 49 Fields: Translation: Cells
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Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem. 2008 Apr 24; 51(8):2502-11.
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. PMID: 18333608.
View in: PubMed Mentions: 56 Fields:
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Community benchmarks for virtual screening. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):193-9.
Irwin JJ. PMID: 18273555.
View in: PubMed Mentions: 38 Fields:
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Has the Performance of Regional-Scale Photochemical Modelling Systems Changed over the Past Decade?. . 2008 Jan 1; 394-403.
C. Hogrefe, J. -Y. Ku, G. Sistla, A. Gilliland, J. S. Irwin, P. S. Porter, E. Gégo, P. Kasibhatla, S. T. Rao. .
View in: Publisher Site Mentions:
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Chemistry in cancer research: a vital partnership. Cancer Res. 2007 Jul 15; 67(14):6539-43.
Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M. PMID: 17621609.
View in: PubMed Mentions: Fields: Translation: HumansAnimals
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Chemistry in cancer research: a vital partnership. ACS Chem Biol. 2007 May 22; 2(5):286-92.
Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M. PMID: 17518428.
View in: PubMed Mentions: 1 Fields: Translation: HumansCells
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Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007 Feb; 25(2):197-206.
Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. PMID: 17287757.
View in: PubMed Mentions: 389 Fields: Translation: Cells
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Objective Reduction of the Space-Time Domain Dimensionality for Evaluating Model Performance. . 2007 Jan 1; 543-552.
Edith Gégo, P. Steven Porter, Christian Hogrefe, R. Gilliam, A. Gilliland, J. Swall, J. Irwin, S. T. Rao. .
View in: Publisher Site Mentions:
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Temporal Signatures of Observations and Model Outputs: Do Time Series Decomposition Methods Capture Relevant Time Scales?. . 2007 Jan 1; 421-429.
P. S. Porter, J. Swall, R. Gillian, E. L. Gego, Christian Hogrefe, A. Gilliland, J. S. Irwin, T. Rao. .
View in: Publisher Site Mentions:
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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.
Christian Hogrefe, J. M. Jones, A. Gilliland, P. Steven Porter, Edith Gégo, R. Gilliam, J. Swall, J. Irwin, S. T. Rao. .
View in: Publisher Site Mentions:
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Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc. 2006 Dec 13; 128(49):15882-91.
Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. PMID: 17147401.
View in: PubMed Mentions: 44 Fields: Translation: Cells
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Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.
Huang N, Shoichet BK, Irwin JJ. PMID: 17154509.
View in: PubMed Mentions: 319 Fields: Translation: Cells
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Temporal features in observed and simulated meteorology and air quality over the Eastern United States. Atmospheric Environment. 2006 Aug 1; 40(26):5041-5055.
C. Hogrefe, P.S. Porter, E. Gego, A. Gilliland, R. Gilliam, J. Swall, J. Irwin, S.T. Rao. .
View in: Publisher Site Mentions:
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An objective comparison of CMAQ and REMSAD performances. Atmospheric Environment. 2006 Aug 1; 40(26):4920-4934.
Edith Gégo, P. Steven Porter, Christian Hogrefe, John S. Irwin. .
View in: Publisher Site Mentions:
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How good is your screening library? Curr Opin Chem Biol. 2006 Aug; 10(4):352-6.
Irwin JJ. PMID: 16797220.
View in: PubMed Mentions: 4 Fields:
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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.
Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP. PMID: 16426060.
View in: PubMed Mentions: 39 Fields: Translation: Cells
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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.
Edith L Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao. .
View in: Publisher Site Mentions:
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Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 2005 Sep 20; 44(37):12316-28.
Irwin JJ, Raushel FM, Shoichet BK. PMID: 16156645.
View in: PubMed Mentions: 43 Fields: Translation: Cells
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Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen. 2005 Oct; 10(7):667-74.
Brenk R, Irwin JJ, Shoichet BK. PMID: 16170052.
View in: PubMed Mentions: 14 Fields: Translation: Cells
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ZINC — A Free Database of Commercially Available Compounds for Virtual Screening. ChemInform. 2005 Apr 19; 36(16).
John J. Irwin, Brian K. Shoichet. .
View in: Publisher Site Mentions:
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Examination of model predictions at different horizontal grid resolutions. Environmental Fluid Mechanics. 2005 Apr 1; 5(1-2):63-85.
Edith Gego, Christian Hogrefe, George Kallos, Antigoni Voudouri, John S. Irwin, S. Trivikrama Rao. .
View in: Publisher Site Mentions:
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Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks. . 2005 Jan 1; 1919-1939.
Edith L. Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao. .
View in: Publisher Site Mentions:
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ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model. 2005 Jan-Feb; 45(1):177-82.
Irwin JJ, Shoichet BK. PMID: 15667143.
View in: PubMed Mentions: 819 Fields: Translation: Cells
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Comparison of the Space-Time Signatures of Air Quality Data From Different Monitoring Networks. . 2004 Jan 1; 481-490.
Edith L. Gego, Christian Hogrefe, P. Steven Porter, John S. Irwin, S. Trivikrama Rao. .
View in: Publisher Site Mentions:
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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.
Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS. PMID: 12556445.
View in: PubMed Mentions: 8 Fields: Translation: AnimalsCells
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Lead discovery using molecular docking. Curr Opin Chem Biol. 2002 Aug; 6(4):439-46.
Shoichet BK, McGovern SL, Wei B, Irwin JJ. PMID: 12133718.
View in: PubMed Mentions: 76 Fields: Translation: HumansAnimalsCells
This graph shows the total number of publications by year. To see the data as text, click here.
This graph shows the total number of publications by year. To return to the graph, click here.
Year | Publications |
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2002 | 1 | 2003 | 1 | 2004 | 1 | 2005 | 7 | 2006 | 6 | 2007 | 6 | 2008 | 7 | 2009 | 8 | 2010 | 5 | 2011 | 4 | 2012 | 4 | 2013 | 4 | 2014 | 4 | 2015 | 3 | 2016 | 2 | 2017 | 2 | 2019 | 1 | 2020 | 7 | 2021 | 1 |
This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
To see the data as text, click here.
This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
To see the data as text, click here.
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