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    John Irwin, PhD

    TitleAcademic Coordinator
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    AddressQB3-BLDG., 1700 4th St.
    San Francisco CA 94143
    Phone415-514-4127

       Bibliographic 
       Publications
      Publications by year:
      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.
      1. Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci U S A. 2013 Apr 2; 110(14):5480-5.
        View in: PubMed
      2. 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.
        View in: PubMed
      3. 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.
        View in: PubMed
      4. Fan H, Irwin JJ, Sali A. Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26.
        View in: PubMed
      5. 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. 2012 Feb; 8(2):144-6.
        View in: PubMed
      6. 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.
        View in: PubMed
      7. 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 Nov; 7(11):769-78.
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      8. 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.
        View in: PubMed
      9. Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry. 2010 Dec 7; 49(48):10267-76.
        View in: PubMed
      10. 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.
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      11. 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 8; 53(13):4891-905.
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      12. 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.
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      13. 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.
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      14. 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.
        View in: PubMed
      15. 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.
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      16. 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.
        View in: PubMed
      17. Irwin JJ. Staring off into chemical space. Nat Chem Biol. 2009 Aug; 5(8):536-7.
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      18. 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.
        View in: PubMed
      19. 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.
        View in: PubMed
      20. Kolb P, Irwin JJ. Docking screens: right for the right reasons? Curr Top Med Chem. 2009; 9(9):755-70.
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      21. Irwin JJ. Using ZINC to acquire a virtual screening library. Curr Protoc Bioinformatics. 2008 Jun; Chapter 14:Unit 14.6.
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      22. 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.
        View in: PubMed
      23. 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.
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      24. Irwin JJ. Community benchmarks for virtual screening. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):193-9.
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      25. 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.
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      26. 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.
        View in: PubMed
      27. 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.
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      28. 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.
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      29. Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801.
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      30. Irwin JJ. How good is your screening library? Curr Opin Chem Biol. 2006 Aug; 10(4):352-6.
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      31. 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.
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      32. Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 2005 Sep 20; 44(37):12316-28.
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      33. 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.
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      34. 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.
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      35. 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.
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      36. Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking. Curr Opin Chem Biol. 2002 Aug; 6(4):439-46.
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