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    Brian Shoichet, PhD

    TitleProfessor
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address1700 4th Street
    San Francisco CA 94158
    Phone415-514-4126
    vCardDownload vCard

      Collapse Biography 
      Collapse Education and Training
      University of California, San FranciscoPh.D. Graduate Division (Pharmaceutical Chemistry)1991
      Collapse Awards and Honors
      1993 - 1996Damon Runyon-Walter Winchell Cancer Research Fellow
      PhRMA Foundation1997 - 1999Career Development Award
      National Science Foundation1998 - 2003CAREER Award
      Northwestern University2001Dean’s Award for Teaching Excellence
      University of Ottawa2004Astra Lectureship
      2006 - 2007Novartis Chemistry Lecturer (Cambridge, Basel, Vienna, Horsham, Tsukuba, Emeryville)
      2008Swiss Universities 3e Cycle en Chimie (Lausanne, Bern, Friborg, Geneva)
      Yale University2009Abbott Lectureship
      2011Society for Biomolecular Sciences Accomplishment Award
      University of Michigan2011Topliss Lectureship

      Collapse Overview 
      Collapse Overview
      The Shoichet lab seeks to discover chemical reagents that can illuminate biological problems. A longstanding effort to do so is by exploiting protein structures to predict new reagents and therapeutic leads (structure-based ligand discovery). Two ongoing projects are 1. Developing new computational methods for ligand discovery and 2. Applying these to G-Protein Coupled Receptors (GPCRs), which are the single largest family of signaling receptors in human cells.

      Allied with this effort is an experimental research program that 3. Tests the new methods in well-controlled systems, determining x-ray crystal structures and measuring binding thermodynamics. The experimental program has led to unexpected discoveries, including the observation that many drugs and reagents can form colloidal aggregates in solution. This has led us to investigate 4. How the physical organic chemistry of drugs affects their behavior in vitro and in vivo, influencing drug delivery and formulation.

      A new effort turns the entire structural view on its head, 5. Developing computational methods to relate receptors by the similarity of their ligands, rather than by protein sequence or structure. This changes pharmacological relationships dramatically—targets that would normally be considered sequence neighbors are pushed far apart (because their ligands are dissimilar), whereas other targets that supposedly have nothing to do with one another become neighbors (because their ligands are very similar). Since the new relationships are articulated by ligands, they may be directly tested both on isolated receptors and, increasingly, against model whole organisms, such as zebra fish, C. elegans and mice. This project seeks to discover the integrated chemical circuits through which drugs and reagents affect whole organisms. "


      Collapse ORNG Applications 
      Collapse Awarded Grants
      Collapse Global Health

      Collapse Bibliographic 
      Collapse Publications
      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.
      List All   |   Timeline
      1. Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S. Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One. 2016; 11(8):e0160365. PMID: 27490099.
        View in: PubMed
      2. O'Meara MJ, Ballouz S, Shoichet BK, Gillis J. Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS One. 2016; 11(7):e0160098. PMID: 27467773.
        View in: PubMed
      3. Shoichet BK, Walters WP, Jiang H, Bajorath J. Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward. J Med Chem. 2016 May 12; 59(9):4033-4. PMID: 27054949.
        View in: PubMed
      4. Irwin JJ, Shoichet BK. Docking Screens for Novel Ligands Conferring New Biology. J Med Chem. 2016 May 12; 59(9):4103-20. PMID: 26913380.
        View in: PubMed
      5. Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL. In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. PLoS One. 2016; 11(3):e0150602. PMID: 26963248.
        View in: PubMed
      6. McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK, Shoichet MS. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes. ACS Chem Biol. 2016 Apr 15; 11(4):992-1000. PMID: 26741163.
        View in: PubMed
      7. Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem. 2016 Feb 25; 59(4):1580-98. PMID: 26699912.
        View in: PubMed
      8. Huang XP, Karpiak J, Kroeze WK, Zhu H, Chen X, Moy SS, Saddoris KA, Nikolova VD, Farrell MS, Wang S, Mangano TJ, Deshpande DA, Jiang A, Penn RB, Jin J, Koller BH, Kenakin T, Shoichet BK, Roth BL. Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. Nature. 2015 Nov 26; 527(7579):477-83. PMID: 26550826.
        View in: PubMed
      9. Arrowsmith CH, Audia JE, Austin C, Baell J, Bennett J, Blagg J, Bountra C, Brennan PE, Brown PJ, Bunnage ME, Buser-Doepner C, Campbell RM, Carter AJ, Cohen P, Copeland RA, Cravatt B, Dahlin JL, Dhanak D, Edwards AM, Frederiksen M, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Ross R, Roth B, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ. Corrigendum: The promise and peril of chemical probes. Nat Chem Biol. 2015 Oct 20; 11(11):887. PMID: 26485080.
        View in: PubMed
      10. Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 2015 Oct 22; 58(20):8285-91. PMID: 26443011.
        View in: PubMed
      11. Barelier S, Sterling T, O'Meara MJ, Shoichet BK. The Recognition of Identical Ligands by Unrelated Proteins. ACS Chem Biol. 2015 Dec 18; 10(12):2772-84. PMID: 26421501.
        View in: PubMed
      12. Pimentel-Elardo SM, Sørensen D, Ho L, Ziko M, Bueler SA, Lu S, Tao J, Moser A, Lee R, Agard D, Fairn G, Rubinstein JL, Shoichet BK, Nodwell JR. Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference. ACS Chem Biol. 2015 Nov 20; 10(11):2616-23. PMID: 26352211; PMCID: PMC4658348 [Available on 11/20/16].
      13. Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM. Prediction and validation of enzyme and transporter off-targets for metformin. J Pharmacokinet Pharmacodyn. 2015 Oct; 42(5):463-75. PMID: 26335661; PMCID: PMC4656030.
      14. Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK. An Aggregation Advisor for Ligand Discovery. J Med Chem. 2015 Sep 10; 58(17):7076-87. PMID: 26295373; PMCID: PMC4646424 [Available on 09/10/16].
      15. Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL. Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents. ACS Chem Biol. 2015 Oct 16; 10(10):2209-18. PMID: 26214585; PMCID: PMC4669066 [Available on 10/16/16].
      16. Arrowsmith CH, Audia JE, Austin C, Baell J, Bennett J, Blagg J, Bountra C, Brennan PE, Brown PJ, Bunnage ME, Buser-Doepner C, Campbell RM, Carter AJ, Cohen P, Copeland RA, Cravatt B, Dahlin JL, Dhanak D, Edwards AM, Frye SV, Gray N, Grimshaw CE, Hepworth D, Howe T, Huber KV, Jin J, Knapp S, Kotz JD, Kruger RG, Lowe D, Mader MM, Marsden B, Mueller-Fahrnow A, Müller S, O'Hagan RC, Overington JP, Owen DR, Rosenberg SH, Roth B, Ross R, Schapira M, Schreiber SL, Shoichet B, Sundström M, Superti-Furga G, Taunton J, Toledo-Sherman L, Walpole C, Walters MA, Willson TM, Workman P, Young RN, Zuercher WJ. The promise and peril of chemical probes. Nat Chem Biol. 2015 Aug; 11(8):536-41. PMID: 26196764.
        View in: PubMed
      17. Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem. 2015 Jul 27; 16(11):1560-4. PMID: 26032594; PMCID: PMC4539595.
      18. Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Homologous ligands accommodated by discrete conformations of a buried cavity. Proc Natl Acad Sci U S A. 2015 Apr 21; 112(16):5039-44. PMID: 25847998; PMCID: PMC4413287.
      19. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. 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
      20. Duan D, Doak AK, Nedyalkova L, Shoichet BK. Colloidal aggregation and the in vitro activity of traditional Chinese medicines. ACS Chem Biol. 2015 Apr 17; 10(4):978-88. PMID: 25606714; PMCID: PMC4646422 [Available on 04/17/16].
      21. London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry. 2015 Jan 20; 54(2):528-37. PMID: 25513739; PMCID: PMC4303301 [Available on 12/16/15].
      22. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J. Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol. 2014 Dec; 10(12):1066-72. PMID: 25344815; PMCID: PMC4232467.
      23. Avasthi P, Onishi M, Karpiak J, Yamamoto R, Mackinder L, Jonikas MC, Sale WS, Shoichet B, Pringle JR, Marshall WF. Actin is required for IFT regulation in Chlamydomonas reinhardtii. Curr Biol. 2014 Sep 8; 24(17):2025-32. PMID: 25155506; PMCID: PMC4160380.
      24. Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM. Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. Biochemistry. 2014 Jul 22; 53(28):4727-38. PMID: 24955762; PMCID: PMC4108184.
      25. Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP. Targeting class A and C serine ß-lactamases with a broad-spectrum boronic acid derivative. J Med Chem. 2014 Jun 26; 57(12):5449-58. PMID: 24882105; PMCID: PMC4079326.
      26. Fischer M, Coleman RG, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem. 2014 Jul; 6(7):575-83. PMID: 24950326; PMCID: PMC4144196.
      27. Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol. 2014 Jul 18; 9(7):1528-35. PMID: 24807704; PMCID: PMC4215856.
      28. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. PMID: 24802635; PMCID: PMC4068255.
      29. Barelier S, Cummings JA, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK. Substrate deconstruction and the nonadditivity of enzyme recognition. J Am Chem Soc. 2014 May 21; 136(20):7374-82. PMID: 24791931; PMCID: PMC4046767.
      30. Cokol M, Weinstein ZB, Yilancioglu K, Tasan M, Doak A, Cansever D, Mutlu B, Li S, Rodriguez-Esteban R, Akhmedov M, Guvenek A, Cokol M, Cetiner S, Giaever G, Iossifov I, Nislow C, Shoichet B, Roth FP. Large-scale identification and analysis of suppressive drug interactions. Chem Biol. 2014 Apr 24; 21(4):541-51. PMID: 24704506; PMCID: PMC4281482.
      31. Shoichet BK. Drug discovery: follow your lead. Nat Chem Biol. 2014 Apr; 10(4):244-5. PMID: 24643239.
        View in: PubMed
      32. Owen SC, Doak AK, Ganesh AN, Nedyalkova L, McLaughlin CK, Shoichet BK, Shoichet MS. Colloidal drug formulations can explain "bell-shaped" concentration-response curves. ACS Chem Biol. 2014 Mar 21; 9(3):777-84. PMID: 24397822; PMCID: PMC3985758.
      33. Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK, Ashrafi K. In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol. 2013 Nov; 11(11):e1001712. PMID: 24260022; PMCID: PMC3833878.
      34. Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One. 2013; 8(10):e75992. PMID: 24098414; PMCID: PMC3787967.
      35. Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17; 52(37):6525-36. PMID: 23972005; PMCID: PMC3813303.
      36. Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. Structure-guided discovery of new deaminase enzymes. J Am Chem Soc. 2013 Sep 18; 135(37):13927-33. PMID: 23968233; PMCID: PMC3827683.
      37. Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol. 2013 Nov 15; 425(22):4569-83. PMID: 23896298; PMCID: PMC3962782.
      38. Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK. Muscarinic receptors as model targets and antitargets for structure-based ligand discovery. Mol Pharmacol. 2013 Oct; 84(4):528-40. PMID: 23887926; PMCID: PMC3781386.
      39. Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities. PLoS One. 2013; 8(7):e69153. PMID: 23874896; PMCID: PMC3715451.
      40. Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ. Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem. 2013 Jul 5; 288(27):19830-44. PMID: 23667258; PMCID: PMC3707686.
      41. Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK. Conformation guides molecular efficacy in docking screens of activated ß-2 adrenergic G protein coupled receptor. ACS Chem Biol. 2013 May 17; 8(5):1018-26. PMID: 23485065; PMCID: PMC3658555.
      42. Merski M, Shoichet BK. The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. J Med Chem. 2013 Apr 11; 56(7):2874-84. PMID: 23473072; PMCID: PMC3624796.
      43. Sassano MF, Doak AK, Roth BL, Shoichet BK. Colloidal aggregation causes inhibition of G protein-coupled receptors. J Med Chem. 2013 Mar 28; 56(6):2406-14. PMID: 23437772; PMCID: PMC3613083.
      44. Cameron RT, Coleman RG, Day JP, Yalla KC, Houslay MD, Adams DR, Shoichet BK, Baillie GS. Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). Biochem Pharmacol. 2013 May 1; 85(9):1297-305. PMID: 23473803; PMCID: PMC3625111.
      45. Lin H, Sassano MF, Roth BL, Shoichet BK. A pharmacological organization of G protein-coupled receptors. Nat Methods. 2013 Feb; 10(2):140-6. PMID: 23291723; PMCID: PMC3560304.
      46. Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc. 2013 Jan 16; 135(2):795-803. PMID: 23256477; PMCID: PMC3557803.
      47. Shoichet BK. Drug discovery: nature's pieces. Nat Chem. 2013 Jan; 5(1):9-10. PMID: 23247169.
        View in: PubMed
      48. Ornelas A, Korczynska M, Ragumani S, Kumaran D, Narindoshvili T, Shoichet BK, Swaminathan S, Raushel FM. Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily. Biochemistry. 2013 Jan 8; 52(1):228-38. PMID: 23214420; PMCID: PMC3542638.
      49. Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F. Fragment-guided design of subnanomolar ß-lactamase inhibitors active in vivo. Proc Natl Acad Sci U S A. 2012 Oct 23; 109(43):17448-53. PMID: 23043117; PMCID: PMC3491531.
      50. Merski M, Shoichet BK. Engineering a model protein cavity to catalyze the Kemp elimination. Proc Natl Acad Sci U S A. 2012 Oct 2; 109(40):16179-83. PMID: 22988064; PMCID: PMC3479533.
      51. 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. PMID: 22716043; PMCID: PMC3405771.
      52. 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. PMID: 22711801; PMCID: PMC3396511.
      53. Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L. Large-scale prediction and testing of drug activity on side-effect targets. Nature. 2012 Jun 21; 486(7403):361-7. PMID: 22722194; PMCID: PMC3383642.
      54. Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK. Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. ACS Chem Biol. 2012 Aug 17; 7(8):1429-35. PMID: 22625864; PMCID: PMC3423826.
      55. Shoichet BK, Kobilka BK. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci. 2012 May; 33(5):268-72. PMID: 22503476; PMCID: PMC3523194.
      56. Mysinger MM, Weiss DR, Ziarek JJ, Gravel S, Doak AK, Karpiak J, Heveker N, Shoichet BK, Volkman BF. Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. Proc Natl Acad Sci U S A. 2012 Apr 3; 109(14):5517-22. PMID: 22431600; PMCID: PMC3325704.
      57. Avasthi P, Marley A, Lin H, Gregori-Puigjane E, Shoichet BK, von Zastrow M, Marshall WF. A chemical screen identifies class a g-protein coupled receptors as regulators of cilia. ACS Chem Biol. 2012 May 18; 7(5):911-9. PMID: 22375814; PMCID: PMC3356477.
      58. Xiang DF, Kolb P, Fedorov AA, Xu C, Fedorov EV, Narindoshivili T, Williams HJ, Shoichet BK, Almo SC, Raushel FM. Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry. 2012 Feb 28; 51(8):1762-73. PMID: 22313111; PMCID: PMC3298459.
      59. 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. PMID: 22179068; PMCID: PMC3262069.
      60. 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. PMID: 22014038; PMCID: PMC3246566.
      61. Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62. PMID: 21999478; PMCID: PMC3238057.
      62. 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. PMID: 21926995; PMCID: PMC3197762.
      63. 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. PMID: 21885739; PMCID: PMC3179104.
      64. Poncet-Montange G, St Martin SJ, Bogatova OV, Prusiner SB, Shoichet BK, Ghaemmaghami S. A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets. J Biol Chem. 2011 Aug 5; 286(31):27718-28. PMID: 21610081; PMCID: PMC3149362.
      65. Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 2011 Feb 23; 133(7):2080-3. PMID: 21275375; PMCID: PMC3043370.
      66. Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry. 2010 Dec 7; 49(48):10267-76. PMID: 21058655; PMCID: PMC2994275.
      67. Eidam O, Romagnoli C, Caselli E, Babaoglu K, Pohlhaus DT, Karpiak J, Bonnet R, Shoichet BK, Prati F. Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as ß-lactamase inhibitors. J Med Chem. 2010 Nov 11; 53(21):7852-63. PMID: 20945905; PMCID: PMC3166525.
      68. 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. PMID: 21048700; PMCID: PMC3055689.
      69. Mysinger MM, Shoichet BK. Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model. 2010 Sep 27; 50(9):1561-73. PMID: 20735049.
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      70. 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. PMID: 20540517; PMCID: PMC2895358.
      71. Doak AK, Wille H, Prusiner SB, Shoichet BK. Colloid formation by drugs in simulated intestinal fluid. J Med Chem. 2010 May 27; 53(10):4259-65. PMID: 20426472; PMCID: PMC2874266.
      72. 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. PMID: 20405927; PMCID: PMC2865168.
      73. Tondi D, Calò S, Shoichet BK, Costi MP. Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors. Bioorg Med Chem Lett. 2010 Jun 1; 20(11):3416-9. PMID: 20452208; PMCID: PMC3177945.
      74. DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD. Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs. J Med Chem. 2010 Mar 25; 53(6):2464-71. PMID: 20180535; PMCID: PMC2867455.
      75. Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 2010 Feb 17; 132(6):1762-3. PMID: 20088583; PMCID: PMC2820149.
      76. Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM. Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase . Biochemistry. 2010 Jan 26; 49(3):611-22. PMID: 20000809; PMCID: PMC2808448.
      77. Mott BT, Ferreira RS, Simeonov A, Jadhav A, Ang KK, Leister W, Shen M, Silveira JT, Doyle PS, Arkin MR, McKerrow JH, Inglese J, Austin CP, Thomas CJ, Shoichet BK, Maloney DJ. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem. 2010 Jan 14; 53(1):52-60. PMID: 19908842; PMCID: PMC2804034.
      78. Jadhav A, Ferreira RS, Klumpp C, Mott BT, Austin CP, Inglese J, Thomas CJ, Maloney DJ, Shoichet BK, Simeonov A. Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem. 2010 Jan 14; 53(1):37-51. PMID: 19908840; PMCID: PMC2992957.
      79. Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol. 2010 Feb 12; 396(1):47-59. PMID: 19913034; PMCID: PMC2815101.
      80. 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. PMID: 19845314; PMCID: PMC2790034.
      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. Predicting new molecular targets for known drugs. Nature. 2009 Nov 12; 462(7270):175-81. PMID: 19881490; PMCID: PMC2784146.
      82. Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK. Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc. 2009 Oct 14; 131(40):14345-54. PMID: 19807181; PMCID: PMC3697005.
      83. Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol. 2009 Dec 11; 394(4):747-63. PMID: 19782087; PMCID: PMC2788029.
      84. 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. PMID: 19719084; PMCID: PMC2745826.
      85. 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. PMID: 19733475; PMCID: PMC2766606.
      86. Ferreira RS, Bryant C, Ang KK, McKerrow JH, Shoichet BK, Renslo AR. Divergent modes of enzyme inhibition in a homologous structure-activity series. J Med Chem. 2009 Aug 27; 52(16):5005-8. PMID: 19637873; PMCID: PMC3760508.
      87. 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. PMID: 19483698; PMCID: PMC2783405.
      88. Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK. Docking for fragment inhibitors of AmpC beta-lactamase. Proc Natl Acad Sci U S A. 2009 May 5; 106(18):7455-60. PMID: 19416920; PMCID: PMC2671983.
      89. Coan KE, Maltby DA, Burlingame AL, Shoichet BK. Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem. 2009 Apr 9; 52(7):2067-75. PMID: 19281222; PMCID: PMC2664636.
      90. 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. PMID: 19342484; PMCID: PMC2672528.
      91. Chen Y, Shoichet BK. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol. 2009 May; 5(5):358-64. PMID: 19305397; PMCID: PMC4006998.
      92. Xiang DF, Kolb P, Fedorov AA, Meier MM, Fedorov LV, Nguyen TT, Sterner R, Almo SC, Shoichet BK, Raushel FM. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry. 2009 Mar 17; 48(10):2237-47. PMID: 19159332; PMCID: PMC3176505.
      93. Chen Y, McReynolds A, Shoichet BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Sci. 2009 Mar; 18(3):662-9. PMID: 19241376; PMCID: PMC2760372.
      94. Marciano DC, Pennington JM, Wang X, Wang J, Chen Y, Thomas VL, Shoichet BK, Palzkill T. Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase. J Mol Biol. 2008 Dec 5; 384(1):151-64. PMID: 18822298; PMCID: PMC2644635.
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      100. Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol. 2008 Mar; 4(3):197-9. PMID: 18223646; PMCID: PMC2730835.
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      102. Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G, Shoichet BK, Costi MP. Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy. J Med Chem. 2007 Nov 15; 50(23):5644-54. PMID: 17956081.
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      103. Delmas J, Chen Y, Prati F, Robin F, Shoichet BK, Bonnet R. Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol. 2008 Jan 4; 375(1):192-201. PMID: 17999931.
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      104. Shoichet BK. No free energy lunch. Nat Biotechnol. 2007 Oct; 25(10):1109-10. PMID: 17921992.
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      105. Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF. O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site. J Am Chem Soc. 2007 Aug 8; 129(31):9548-9. PMID: 17628063.
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      107. Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 2007 Aug 24; 371(4):1118-34. PMID: 17599350; PMCID: PMC2104542.
      108. Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 2007 Jun 12; 46(23):6688-95. PMID: 17503785.
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      109. Feng BY, Simeonov A, Jadhav A, Babaoglu K, Inglese J, Shoichet BK, Austin CP. A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem. 2007 May 17; 50(10):2385-90. PMID: 17447748.
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      110. Chen Y, Bonnet R, Shoichet BK. The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution. J Am Chem Soc. 2007 May 2; 129(17):5378-80. PMID: 17408273; PMCID: PMC2577156.
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      113. Coan KE, Shoichet BK. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst. 2007 Mar; 3(3):208-13. PMID: 17308667.
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      114. Shoichet BK. Interpreting steep dose-response curves in early inhibitor discovery. J Med Chem. 2006 Dec 14; 49(25):7274-7. PMID: 17149857.
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      115. Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM. Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library. J Am Chem Soc. 2006 Dec 13; 128(49):15892-902. PMID: 17147402.
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      116. 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. PMID: 17147401.
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      117. Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem. 2006 Nov 16; 49(23):6789-801. PMID: 17154509; PMCID: PMC3383317.
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      119. Leach AR, Shoichet BK, Peishoff CE. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem. 2006 Oct 5; 49(20):5851-5. PMID: 17004700.
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      137. Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol. 2004 Apr 9; 337(5):1161-82. PMID: 15046985.
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      138. Horn JR, Shoichet BK. Allosteric inhibition through core disruption. J Mol Biol. 2004 Mar 5; 336(5):1283-91. PMID: 15037085.
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      139. Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK. Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Biochemistry. 2003 Dec 16; 42(49):14483-91. PMID: 14661960.
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      140. Seidler J, McGovern SL, Doman TN, Shoichet BK. Identification and prediction of promiscuous aggregating inhibitors among known drugs. J Med Chem. 2003 Oct 9; 46(21):4477-86. PMID: 14521410.
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      141. McGovern SL, Helfand BT, Feng B, Shoichet BK. A specific mechanism of nonspecific inhibition. J Med Chem. 2003 Sep 25; 46(20):4265-72. PMID: 13678405.
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      142. Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S. Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. J Am Chem Soc. 2003 Aug 13; 125(32):9612-8. PMID: 12904027.
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      143. Wang X, Minasov G, Blázquez J, Caselli E, Prati F, Shoichet BK. Recognition and resistance in TEM beta-lactamase. Biochemistry. 2003 Jul 22; 42(28):8434-44. PMID: 12859188.
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      144. McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem. 2003 Jul 3; 46(14):2895-907. PMID: 12825931.
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      145. McGovern SL, Shoichet BK. Kinase inhibitors: not just for kinases anymore. J Med Chem. 2003 Apr 10; 46(8):1478-83. PMID: 12672248.
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      146. Soelaiman S, Wei BQ, Bergson P, Lee YS, Shen Y, Mrksich M, Shoichet BK, Tang WJ. Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J Biol Chem. 2003 Jul 11; 278(28):25990-7. PMID: 12676933.
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      147. 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. PMID: 12556445.
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      149. Beadle BM, Shoichet BK. Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother. 2002 Dec; 46(12):3978-80. PMID: 12435704; PMCID: PMC132770.
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      151. Trehan I, Morandi F, Blaszczak LC, Shoichet BK. Using steric hindrance to design new inhibitors of class C beta-lactamases. Chem Biol. 2002 Sep; 9(9):971-80. PMID: 12323371.
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      152. Beadle BM, Shoichet BK. Structural bases of stability-function tradeoffs in enzymes. J Mol Biol. 2002 Aug 9; 321(2):285-96. PMID: 12144785.
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      156. Wang X, Minasov G, Shoichet BK. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol. 2002 Jun 28; 320(1):85-95. PMID: 12079336.
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      157. Wang X, Minasov G, Shoichet BK. The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem. 2002 Aug 30; 277(35):32149-56. PMID: 12058046.
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      158. Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci. 2002 Jun; 11(6):1393-408. PMID: 12021438; PMCID: PMC2373613.
      159. Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem. 2002 May 23; 45(11):2213-21. PMID: 12014959.
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      160. Minasov G, Wang X, Shoichet BK. An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc. 2002 May 15; 124(19):5333-40. PMID: 11996574.
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      161. McGovern SL, Caselli E, Grigorieff N, Shoichet BK. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem. 2002 Apr 11; 45(8):1712-22. PMID: 11931626.
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      162. Wang X, Minasov G, Shoichet BK. Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams. Proteins. 2002 Apr 1; 47(1):86-96. PMID: 11870868.
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      163. Beadle BM, Trehan I, Focia PJ, Shoichet BK. Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Structure. 2002 Mar; 10(3):413-24. PMID: 12005439.
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      164. Powers RA, Caselli E, Focia PJ, Prati F, Shoichet BK. Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design. Biochemistry. 2001 Aug 7; 40(31):9207-14. PMID: 11478888.
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      165. Trehan I, Beadle BM, Shoichet BK. Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site. Biochemistry. 2001 Jul 10; 40(27):7992-9. PMID: 11434768.
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      169. Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK. Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases. Chem Biol. 2001 Jan; 8(1):17-31. PMID: 11182316.
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      173. Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry. 1999 Feb 23; 38(8):2570-6. PMID: 10029552.
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      174. Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP. Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry. 1999 Feb 2; 38(5):1607-17. PMID: 9931028.
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      180. Shoichet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction. Chem Biol. 1996 Mar; 3(3):151-6. PMID: 8807840.
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      181. Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol. 1996 Mar; 3(3):233-9. PMID: 8605624.
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      182. Zhang XJ, Baase WA, Shoichet BK, Wilson KP, Matthews BW. Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive. Protein Eng. 1995 Oct; 8(10):1017-22. PMID: 8771182.
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      183. Shoichet BK, Baase WA, Kuroki R, Matthews BW. A relationship between protein stability and protein function. Proc Natl Acad Sci U S A. 1995 Jan 17; 92(2):452-6. PMID: 7831309; PMCID: PMC42758.
      184. Schellenberger U, Balaram P, Francis VS, Shoichet BK, Santi DV. Partial restoration of activity to Lactobacillus casei thymidylate synthase following inactivation by domain deletion. Biochemistry. 1994 May 10; 33(18):5623-9. PMID: 8180187.
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      185. Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Eng. 1993 Sep; 6(7):723-32. PMID: 7504257.
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      186. Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science. 1993 Mar 5; 259(5100):1445-50. PMID: 8451640.
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      187. Shoichet BK, Kuntz ID. Protein docking and complementarity. J Mol Biol. 1991 Sep 5; 221(1):327-46. PMID: 1920412.
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      188. Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P. Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis. Protein Eng. 1989 Nov; 3(2):95-103. PMID: 2594728.
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