John Irwin, PhD

Title(s)Adjunct Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address1700 4th St, #508A
San Francisco CA 94158
Phone415-878-1705
ORCID ORCID Icon0000-0002-1195-6417 Additional info
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    Collapse Research Activities and Funding
    Ultra-large library docking for ligand discovery
    NIH R01GM133836Sep 27, 2019 - Aug 31, 2023
    Role: Principal Investigator
    A Web-Based Automatic Virtual Screening System
    NIH R01GM071896Aug 1, 2004 - Apr 30, 2025
    Role: Co-Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details 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. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Structure-based discovery of CFTR potentiators and inhibitors. bioRxiv. 2024 Mar 11. 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. PMID: 37745391; PMCID: PMC10515777.
      View in: PubMed   Mentions:
    2. Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor. bioRxiv. 2024 Mar 06. 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. PMID: 38234749; PMCID: PMC10793424.
      View in: PubMed   Mentions:
    3. Large library docking for cannabinoid-1 receptor agonists with reduced side effects. bioRxiv. 2024 Feb 28. 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. PMID: 38328157; PMCID: PMC10849508.
      View in: PubMed   Mentions:
    4. Docking for molecules that bind in a symmetric stack to Alzheimer’s disease tau fibrils with SymDOCK. Biophysical Journal. 2024 Feb 1; 123(3):298a. Smith SM, Kunach KP, Knight KI, Kormos KR, Pepe PJ, Glenn GI, Irwin IJ, DeGrado DW, Diamond DM, Shahmoradian SS, Shoichet SB. .
      View in: Publisher Site   Mentions:
    5. DockOpt: A Tool for Automatic Optimization of Docking Models. J Chem Inf Model. 2024 Feb 12; 64(3):1004-1016. Knight IS, Mailhot O, Tang KG, Irwin JJ. PMID: 38206771; PMCID: PMC10865354.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    6. Docking for Molecules That Bind in a Symmetric Stack with SymDOCK. J Chem Inf Model. 2024 Jan 22; 64(2):425-434. Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK. PMID: 38191997; PMCID: PMC10806807.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. AlphaFold2 structures template ligand discovery. bioRxiv. 2023 Dec 21. 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. PMID: 38187536; PMCID: PMC10769324.
      View in: PubMed   Mentions:
    8. Docking for EP4R antagonists active against inflammatory pain. Nat Commun. 2023 Dec 06; 14(1):8067. 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. PMID: 38057319; PMCID: PMC10700596.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    9. Docking for molecules that bind in a symmetric stack with SymDOCK. bioRxiv. 2023 Oct 29. Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK. PMID: 37961414; PMCID: PMC10634874.
      View in: PubMed   Mentions:
    10. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci. 2023 08; 32(8):e4712. Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons LM, Lorenzo-Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García-Sastre A, Shoichet BK, Craik CS. PMID: 37354015; PMCID: PMC10364469.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCellsPHPublic Health
    11. Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase. J Med Chem. 2023 06 22; 66(12):7785-7803. 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. PMID: 37294077; PMCID: PMC10374283.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    12. Structure-based discovery of conformationally selective inhibitors of the serotonin transporter. Cell. 2023 05 11; 186(10):2160-2175.e17. 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. PMID: 37137306; PMCID: PMC10306110.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    13. Large-Scale Docking in the Cloud. J Chem Inf Model. 2023 05 08; 63(9):2735-2741. Tingle BI, Irwin JJ. PMID: 37071086; PMCID: PMC10170500.
      View in: PubMed   Mentions: 1     Fields:    
    14. ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery. J Chem Inf Model. 2023 02 27; 63(4):1166-1176. Tingle BI, Tang KG, Castanon M, Gutierrez JJ, Khurelbaatar M, Dandarchuluun C, Moroz YS, Irwin JJ. PMID: 36790087; PMCID: PMC9976280.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    15. Modeling the expansion of virtual screening libraries. Nat Chem Biol. 2023 06; 19(6):712-718. Lyu J, Irwin JJ, Shoichet BK. PMID: 36646956; PMCID: PMC10243288.
      View in: PubMed   Mentions: 12     Fields:    
    16. 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 01 10; 120(2):e2212931120. 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. PMID: 36598939; PMCID: PMC9926234.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCellsPHPublic Health
    17. Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor. Science. 2022 09 30; 377(6614):eabn7065. 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. PMID: 36173843; PMCID: PMC10360211.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    18. Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity. Nature. 2022 10; 610(7932):582-591. Kaplan AL, Confair DN, Kim K, Barros-Álvarez X, Rodriguiz RM, Yang Y, Kweon OS, Che T, McCorvy JD, Kamber DN, Phelan JP, Martins LC, Pogorelov VM, DiBerto JF, Slocum ST, Huang XP, Kumar JM, Robertson MJ, Panova O, Seven AB, Wetsel AQ, Wetsel WC, Irwin JJ, Skiniotis G, Shoichet BK, Roth BL, Ellman JA. PMID: 36171289; PMCID: PMC9996387.
      View in: PubMed   Mentions: 47     Fields:    Translation:Animals
    19. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv. 2022 Jul 28. 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. PMID: 35794891; PMCID: PMC9258288.
      View in: PubMed   Mentions:
    20. Drug building blocks and libraries at risk in Ukraine. Science. 2022 05 27; 376(6596):929. Kondratov IS, Moroz YS, Irwin JJ, Shoichet BK. PMID: 35617394.
      View in: PubMed   Mentions:    Fields:    
    21. CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nat Rev Chem. 2022 Apr; 6(4):287-295. Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM. PMID: 35783295; PMCID: PMC9246350.
      View in: PubMed   Mentions: 10  
    22. Publisher Correction: A practical guide to large-scale docking. Nat Protoc. 2022 Jan; 17(1):177. Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK. PMID: 34887579.
      View in: PubMed   Mentions: 1     Fields:    
    23. Structures of the σ2 receptor enable docking for bioactive ligand discovery. Nature. 2021 Dec; 600(7890):759-764. 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. PMID: 34880501; PMCID: PMC8867396.
      View in: PubMed   Mentions: 49     Fields:    Translation:Animals
    24. A practical guide to large-scale docking. Nat Protoc. 2021 10; 16(10):4799-4832. Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK. PMID: 34561691; PMCID: PMC8522653.
      View in: PubMed   Mentions: 100     Fields:    
    25. Ligand Strain Energy in Large Library Docking. J Chem Inf Model. 2021 09 27; 61(9):4331-4341. Gu S, Smith MS, Yang Y, Irwin JJ, Shoichet BK. PMID: 34467754; PMCID: PMC8501943.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    26. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 04; 7(16). Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. PMID: 33853786; PMCID: PMC8046379.
      View in: PubMed   Mentions: 62     Fields:    Translation:HumansCells
    27. Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model. 2021 02 22; 61(2):699-714. Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. PMID: 33494610; PMCID: PMC7913603.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    28. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv. 2020 Nov 24. Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, QCRG Structural Biology Consortium, Aimon A, Bennett JM, Neto JB, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Johannes Gregor Matthias Rack, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. PMID: 33269349; PMCID: PMC7709169.
      View in: PubMed   Mentions:
    29. ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J Chem Inf Model. 2020 12 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; PMCID: PMC8284596.
      View in: PubMed   Mentions: 148     Fields:    
    30. 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; PMCID: PMC7960226.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    31. 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. Glatfelter GG, Stein SR, Kang KH, Jones JA, Irwin IJ, Roth RB, Shoichet SB, Dubocovich DM. .
      View in: Publisher Site   Mentions:
    32. 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; PMCID: PMC7136196.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    33. 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; PMCID: PMC7134359.
      View in: PubMed   Mentions: 107     Fields:    Translation:HumansAnimals
    34. 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: 6     Fields:    Translation:HumansCells
    35. 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; PMCID: PMC6383769.
      View in: PubMed   Mentions: 255     Fields:    Translation:Humans
    36. 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; PMCID: PMC5780839.
      View in: PubMed   Mentions: 14     Fields:    
    37. 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; PMCID: PMC5835362.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    38. Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One. 2016; 11(8):e0160365. Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S. PMID: 27490099; PMCID: PMC4973902.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimals
    39. Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 05 12; 59(9):4103-20. Irwin JJ, Shoichet BK. PMID: 26913380; PMCID: PMC4865415.
      View in: PubMed   Mentions: 100     Fields:    
    40. ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015 Nov 23; 55(11):2324-37. Sterling T, Irwin JJ. PMID: 26479676; PMCID: PMC4658288.
      View in: PubMed   Mentions: 926     Fields:    Translation:HumansAnimals
    41. An Aggregation Advisor for Ligand Discovery. J Med Chem. 2015 Sep 10; 58(17):7076-87. Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK. PMID: 26295373; PMCID: PMC4646424.
      View in: PubMed   Mentions: 152     Fields:    
    42. Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2015 Mar; 11(3):235. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. PMID: 25689339.
      View in: PubMed   Mentions:    Fields:    
    43. Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Dec; 10(12):1066-72. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. PMID: 25344815; PMCID: PMC4232467.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansAnimalsCells
    44. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol. 2014 Jul 18; 9(7):1528-35. Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G. PMID: 24807704; PMCID: PMC4215856.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    45. 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. Silber BM, Gever JR, Rao S, Li Z, Renslo AR, Widjaja K, Wong C, Giles K, Freyman Y, Elepano M, Irwin JJ, Jacobson MP, Prusiner SB. PMID: 24530226; PMCID: PMC3984052.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    46. Covalent Docking of Large Libraries for the Discovery of Chemical Probes. Biophysical Journal. 2014 Jan 1; 106(2):264a. London LN, Miller MR, Irwin IJ, Eidam EO, Gibold GL, Bonnet BR, Shoichet SB, Taunton TJ. .
      View in: Publisher Site   Mentions:
    47. Ligand pose and orientational sampling in molecular docking. PLoS One. 2013; 8(10):e75992. Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. PMID: 24098414; PMCID: PMC3787967.
      View in: PubMed   Mentions: 76     Fields:    Translation:Cells
    48. Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells. Bioorg Med Chem. 2013 Dec 15; 21(24):7999-8012. Silber BM, Gever JR, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB. PMID: 24183589; PMCID: PMC3984054.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    49. Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem. 2013 Jul 05; 288(27):19830-44. Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ. PMID: 23667258; PMCID: PMC3707686.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    50. 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. Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM. PMID: 23509259; PMCID: PMC3619328.
      View in: PubMed   Mentions: 87     Fields:    Translation:HumansCells
    51. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem. 2012 Jul 26; 55(14):6582-94. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. PMID: 22716043; PMCID: PMC3405771.
      View in: PubMed   Mentions: 660     Fields:    Translation:HumansCells
    52. Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A. 2012 Jul 10; 109(28):11178-83. Gregori-Puigjané E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK. PMID: 22711801; PMCID: PMC3396511.
      View in: PubMed   Mentions: 75     Fields:    Translation:Humans
    53. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012 Jul 23; 52(7):1757-68. Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. PMID: 22587354; PMCID: PMC3402020.
      View in: PubMed   Mentions: 761     Fields:    
    54. Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26. Fan H, Irwin JJ, Sali A. PMID: 22183533; PMCID: PMC3386294.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    55. Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol. 2011 Dec 18; 8(2):144-6. Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK. PMID: 22179068; PMCID: PMC3262069.
      View in: PubMed   Mentions: 52     Fields:    Translation:Animals
    56. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92. Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. PMID: 22014038; PMCID: PMC3246566.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    57. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Sep 18; 7(11):769-78. Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK. PMID: 21926995; PMCID: PMC3197762.
      View in: PubMed   Mentions: 126     Fields:    Translation:Cells
    58. 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. Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A. PMID: 21885739; PMCID: PMC3179104.
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    59. The chemical basis of pharmacology. Biochemistry. 2010 Dec 07; 49(48):10267-76. Keiser MJ, Irwin JJ, Shoichet BK. PMID: 21058655; PMCID: PMC2994275.
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    60. 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; PMCID: PMC3055689.
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    61. 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; PMCID: PMC2895358.
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    62. 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; PMCID: PMC2865168.
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    63. 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; PMCID: PMC3066450.
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    64. 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; PMCID: PMC2784146.
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    65. 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; PMCID: PMC2790034.
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    66. 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; PMCID: PMC2745826.
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    67. 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; PMCID: PMC2766606.
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    68. Staring off into chemical space. Nat Chem Biol. 2009 Aug; 5(8):536-7. Irwin JJ. PMID: 19620992; PMCID: PMC2749036.
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    69. 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; PMCID: PMC2783405.
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    70. 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; PMCID: PMC2672528.
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    71. Docking screens: right for the right reasons? Curr Top Med Chem. 2009; 9(9):755-70. Kolb P, Irwin JJ. PMID: 19754393; PMCID: PMC3383315.
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    72. ChemInform Abstract: Quantifying the Relationships among Drug Classes. ChemInform. 2008 Jul 15; 39(29). Hert HJ, Keiser KM, Irwin IJ, Oprea OT, Shoichet SB. .
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    73. 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 IJ, Civerolo CK, Hogrefe HC, Appel AW, Foley FK, Swall SJ. .
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    74. Using ZINC to acquire a virtual screening library. Curr Protoc Bioinformatics. 2008 Jun; Chapter 14:Unit 14.6. Irwin JJ. PMID: 18551414.
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    75. 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; PMCID: PMC2722950.
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    76. 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; PMCID: PMC2655312.
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    77. Community benchmarks for virtual screening. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):193-9. Irwin JJ. PMID: 18273555.
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    78. Has the Performance of Regional-Scale Photochemical Modelling Systems Changed over the Past Decade?. . 2008 Jan 1; 394-403. Hogrefe HC, Ku KJ, Sistla SG, Gilliland GA, Irwin IJ, Porter PP, Gégo GE, Kasibhatla KP, Rao RS. .
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    79. 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.
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    80. 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.
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    81. 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.
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    82. Temporal Signatures of Observations and Model Outputs: Do Time Series Decomposition Methods Capture Relevant Time Scales?. . 2007 Jan 1; 421-429. Porter PP, Swall SJ, Gillian GR, Gego GE, Hogrefe HC, Gilliland GA, Irwin IJ, Rao RT. .
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    83. 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. Hogrefe HC, Jones JJ, Gilliland GA, Porter PP, Gégo GE, Gilliam GR, Swall SJ, Irwin IJ, Rao RS. .
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    84. Objective Reduction of the Space-Time Domain Dimensionality for Evaluating Model Performance. . 2007 Jan 1; 543-552. Gégo GE, Porter PP, Hogrefe HC, Gilliam GR, Gilliland GA, Swall SJ, Irwin IJ, Rao RS. .
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    85. 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.
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    86. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801. Huang N, Shoichet BK, Irwin JJ. PMID: 17154509; PMCID: PMC3383317.
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    87. An objective comparison of CMAQ and REMSAD performances. Atmospheric Environment. 2006 Aug 1; 40(26):4920-4934. Gégo GE, Porter PP, Hogrefe HC, Irwin IJ. .
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    88. Temporal features in observed and simulated meteorology and air quality over the Eastern United States. Atmospheric Environment. 2006 Aug 1; 40(26):5041-5055. Hogrefe HC, Porter PP, Gego GE, Gilliland GA, Gilliam GR, Swall SJ, Irwin IJ, Rao RS. .
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    89. How good is your screening library? Curr Opin Chem Biol. 2006 Aug; 10(4):352-6. Irwin JJ. PMID: 16797220.
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    90. 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.
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    91. 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. Gego GE, Porter PP, Irwin IJ, Hogrefe HC, Rao RS. .
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    92. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 2005 Sep 20; 44(37):12316-28. Irwin JJ, Raushel FM, Shoichet BK. PMID: 16156645.
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    93. 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; PMCID: PMC1532927.
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    94. ZINC — A Free Database of Commercially Available Compounds for Virtual Screening. ChemInform. 2005 Apr 19; 36(16). Irwin IJ, Shoichet SB. .
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    95. Examination of model predictions at different horizontal grid resolutions. Environmental Fluid Mechanics. 2005 Apr 1; 5(1-2):63-85. Gego GE, Hogrefe HC, Kallos KG, Voudouri VA, Irwin IJ, Rao RS. .
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    96. Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks. . 2005 Jan 1; 1919-1939. Gego GE, Porter PP, Irwin IJ, Hogrefe HC, Rao RS. .
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    97. 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; PMCID: PMC1360656.
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    98. Comparison of the Space-Time Signatures of Air Quality Data From Different Monitoring Networks. . 2004 Jan 1; 481-490. Gego GE, Hogrefe HC, Porter PP, Irwin IJ, Rao RS. .
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    99. 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: 10     Fields:    Translation:AnimalsCells
    100. 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.
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