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John Irwin, PhD

Title(s)Adjunct Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address1700 4th St
San Francisco CA 94158
Phone415-878-1705
ORCID ORCID Icon0000-0002-1195-6417 Additional info
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    Ultra-large library docking for ligand discovery
    NIH/NIGMS R01GM133836Sep 27, 2019 - Aug 31, 2023
    Role: Principal Investigator
    A Web-Based Automatic Virtual Screening System
    NIH/NIGMS R01GM071896Aug 1, 2004 - May 31, 2016
    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. 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:    Fields:    
    2. 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:
    3. Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. J Am Chem Soc. 2020 Mar 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:    Fields:    
    4. 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: 2     Fields:    Translation:HumansAnimals
    5. Docking Finds GPCR Ligands in Dark Chemical Matter. J Med Chem. 2020 Jan 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
    6. 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: 17     Fields:    Translation:Humans
    7. 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:    Fields:    
    8. 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: 10     Fields:    Translation:HumansCells
    9. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    10. Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 05 12; 59(9):4103-20. Irwin JJ, Shoichet BK. PMID: 26913380.
      View in: PubMed   Mentions: 32     Fields:    
    11. ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015 Nov 23; 55(11):2324-37. Sterling T, Irwin JJ. PMID: 26479676.
      View in: PubMed   Mentions: 110     Fields:    Translation:HumansAnimals
    12. 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.
      View in: PubMed   Mentions: 50     Fields:    
    13. 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:    
    14. 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.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    15. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    16. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    17. 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:
    18. 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.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    19. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    20. 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.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    21. 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.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    22. 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.
      View in: PubMed   Mentions: 223     Fields:    Translation:HumansCells
    23. 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.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    24. 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.
      View in: PubMed   Mentions: 429     Fields:    
    25. Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26. Fan H, Irwin JJ, Sali A. PMID: 22183533.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    26. 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.
      View in: PubMed   Mentions: 43     Fields:    Translation:Animals
    27. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    28. 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.
      View in: PubMed   Mentions: 100     Fields:    Translation:Cells
    29. 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.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    30. 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
    31. 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: 34     Fields:    Translation:AnimalsCells
    32. 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: 39     Fields:    Translation:Humans
    33. 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: 66     Fields:    Translation:HumansCells
    34. 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:
    35. 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: 50     Fields:    Translation:Cells
    36. 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: 416     Fields:    Translation:HumansAnimals
    37. 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: 69     Fields:    Translation:Cells
    38. 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: 48     Fields:    Translation:Cells
    39. Staring off into chemical space. Nat Chem Biol. 2009 Aug; 5(8):536-7. Irwin JJ. PMID: 19620992.
      View in: PubMed   Mentions: 1     Fields:    
    40. 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: 45     Fields:    Translation:Cells
    41. 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: 96     Fields:    Translation:Cells
    42. 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
    43. 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:
    44. 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:    
    45. 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: 44     Fields:    Translation:Cells
    46. 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: 53     Fields:    
    47. 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: 36     Fields:    
    48. 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
    49. 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
    50. 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: 332     Fields:    Translation:Cells
    51. 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
    52. 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: 297     Fields:    Translation:Cells
    53. 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:    
    54. 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: 36     Fields:    Translation:Cells
    55. 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: 42     Fields:    Translation:Cells
    56. 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: 12     Fields:    Translation:Cells
    57. 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:
    58. 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: 743     Fields:    Translation:Cells
    59. 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
    60. 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: 73     Fields:    Translation:HumansAnimalsCells
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