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Brian K. Shoichet, Ph.D. - Publications

Affiliations: 
1996-2002 Chemistry Northwestern University, Evanston, IL 
 2002- Chemistry University of California, San Francisco, San Francisco, CA 
Area:
GPCR, computational chemistry
Website:
http://shoichetlab.compbio.ucsf.edu/

212 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 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. Ultra-large library docking for discovering new chemotypes. Nature. PMID 30728502 DOI: 10.1038/s41586-019-0917-9  0.76
2018 Liu H, Hofmann J, Fish I, Schaake B, Eitel K, Bartuschat A, Kaindl J, Rampp H, Banerjee A, Hübner H, Clark MJ, Vincent SG, Fisher JT, Heinrich MR, Hirata K, ... ... Shoichet BK, et al. Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists. Proceedings of the National Academy of Sciences of the United States of America. PMID 30404914 DOI: 10.1073/pnas.1813988115  0.72
2018 Pottel J, Levit A, Korczynska M, Fischer M, Shoichet BK. The Recognition of Unrelated Ligands by Individual Proteins. Acs Chemical Biology. PMID 30095890 DOI: 10.1021/acschembio.8b00443  0.76
2018 Weiss DR, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK. Selectivity Challenges in Docking Screens for GPCR Targets and Anti-Targets. Journal of Medicinal Chemistry. PMID 29990431 DOI: 10.1021/acs.jmedchem.8b00718  0.36
2018 Wang S, Che T, Levit A, Shoichet BK, Wacker D, Roth BL. Structure of the Ddopamine receptor bound to the atypical antipsychotic drug risperidone. Nature. PMID 29466326 DOI: 10.1038/nature25758  0.36
2018 Korczynska M, Clark MJ, Valant C, Xu J, Moo EV, Albold S, Weiss DR, Torosyan H, Huang W, Kruse AC, Lyda BR, May LT, Baltos JA, Sexton PM, Kobilka BK, ... ... Shoichet BK, et al. Structure-based discovery of selective positive allosteric modulators of antagonists for the Mmuscarinic acetylcholine receptor. Proceedings of the National Academy of Sciences of the United States of America. PMID 29453275 DOI: 10.1073/pnas.1718037115  0.48
2018 Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, ... ... Shoichet BK, et al. Prediction of enzymatic pathways by integrative pathway mapping. Elife. 7. PMID 29377793 DOI: 10.7554/eLife.31097  0.68
2017 McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL. Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. Nature Chemical Biology. PMID 29227473 DOI: 10.1038/nchembio.2527  0.32
2017 McCorvy JD, Butler KV, Kelly B, Rechsteiner K, Karpiak J, Betz RM, Kormos BL, Shoichet BK, Dror RO, Jin J, Roth BL. Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. Nature Chemical Biology. PMID 29227473 DOI: 10.1038/nchembio.2527  0.32
2017 Fish I, Stoessel A, Eitel K, Valant C, Albold S, Hübner H, Möller D, Clark MJ, Sunahara RK, Christopoulos A, Shoichet BK, Gmeiner P. Structure-based design and discovery of new M2 receptor agonists. Journal of Medicinal Chemistry. PMID 29094937 DOI: 10.1021/acs.jmedchem.7b01113  0.72
2017 Wang S, Wacker D, Levit A, Che T, Betz RM, McCorvy JD, Venkatakrishnan AJ, Huang XP, Dror RO, Shoichet BK, Roth BL. D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. Science (New York, N.Y.). 358: 381-386. PMID 29051383 DOI: 10.1126/science.aan5468  0.36
2017 Roth BL, Irwin JJ, Shoichet BK. Discovery of new GPCR ligands to illuminate new biology. Nature Chemical Biology. 13: 1143-1151. PMID 29045379 DOI: 10.1038/nchembio.2490  0.76
2017 Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. Proceedings of the National Academy of Sciences of the United States of America. PMID 28760952 DOI: 10.1073/pnas.1703287114  0.76
2017 Lansu K, Karpiak J, Liu J, Huang XP, McCorvy JD, Kroeze WK, Che T, Nagase H, Carroll FI, Jin J, Shoichet BK, Roth BL. In silico design of novel probes for the atypical opioid receptor MRGPRX2. Nature Chemical Biology. PMID 28288109 DOI: 10.1038/nchembio.2334  0.36
2017 Wacker D, Wang S, McCorvy JD, Betz RM, Venkatakrishnan AJ, Levit A, Lansu K, Schools ZL, Che T, Nichols DE, Shoichet BK, Dror RO, Roth BL. Crystal Structure of an LSD-Bound Human Serotonin Receptor. Cell. 168: 377-389.e12. PMID 28129538 DOI: 10.1016/j.cell.2016.12.033  0.36
2016 Lee H, Fischer M, Shoichet BK, Liu SY. Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics. Journal of the American Chemical Society. PMID 27603116 DOI: 10.1021/jacs.6b06566  0.76
2016 Irwin JJ, Pottel J, Zou L, Wen H, Zuk S, Zhang X, Sterling T, Shoichet BK, Lionberger R, Giacomini KM. A Molecular Basis for Innovation in Drug Excipients. Clinical Pharmacology and Therapeutics. PMID 27557422 DOI: 10.1002/cpt.458  0.76
2016 Manglik A, Lin H, Aryal DK, McCorvy JD, Dengler D, Corder G, Levit A, Kling RC, Bernat V, Hübner H, Huang XP, Sassano MF, Giguère PM, Löber S, Da Duan, ... ... Shoichet BK, et al. Structure-based discovery of opioid analgesics with reduced side effects. Nature. 1-6. PMID 27533032 DOI: 10.1038/nature19112  0.48
2016 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. 11: e0160365. PMID 27490099 DOI: 10.1371/journal.pone.0160365  0.76
2016 O'Meara MJ, Ballouz S, Shoichet BK, Gillis J. Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. Plos One. 11: e0160098. PMID 27467773 DOI: 10.1371/journal.pone.0160098  0.4
2016 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, ... ... Shoichet BK, et al. In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. Plos One. 11: e0150602. PMID 26963248 DOI: 10.1371/journal.pone.0150602  1
2016 Irwin JJ, Shoichet BK. Docking screens for novel ligands conferring new biology. Journal of Medicinal Chemistry. PMID 26913380 DOI: 10.1021/acs.jmedchem.5b02008  0.76
2015 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. Journal of Medicinal Chemistry. PMID 26699912 DOI: 10.1021/acs.jmedchem.5b01527  1
2015 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, ... ... Shoichet BK, et al. Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. Nature. PMID 26550826 DOI: 10.1038/nature15699  1
2015 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. Journal of Medicinal Chemistry. 58: 8285-91. PMID 26443011 DOI: 10.1021/acs.jmedchem.5b01216  1
2015 Barelier S, Sterling T, O'Meara MJ, Shoichet BK. The Recognition of Identical Ligands by Unrelated Proteins. Acs Chemical Biology. PMID 26421501 DOI: 10.1021/acschembio.5b00683  1
2015 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 Chemical Biology. PMID 26352211 DOI: 10.1021/acschembio.5b00612  1
2015 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. Journal of Pharmacokinetics and Pharmacodynamics. PMID 26335661 DOI: 10.1007/s10928-015-9436-y  1
2015 Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK. An Aggregation Advisor for Ligand Discovery. Journal of Medicinal Chemistry. PMID 26295373 DOI: 10.1021/acs.jmedchem.5b01105  1
2015 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, ... ... Shoichet B, et al. The promise and peril of chemical probes. Nature Chemical Biology. 11: 536-41. PMID 26196764 DOI: 10.1038/nchembio.1867  1
2015 Fischer M, Shoichet BK, Fraser JS. One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem : a European Journal of Chemical Biology. PMID 26032594 DOI: 10.1002/cbic.201500196  1
2015 Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Homologous ligands accommodated by discrete conformations of a buried cavity. Proceedings of the National Academy of Sciences of the United States of America. 112: 5039-44. PMID 25847998 DOI: 10.1073/pnas.1500806112  1
2015 London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimerman?i? P, Bonnet R, Shoichet BK, Taunton J. Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nature Chemical Biology. 11: 235. PMID 25689339 DOI: 10.1038/nchembio0315-235b  0.76
2015 Duan D, Doak AK, Nedyalkova L, Shoichet BK. Colloidal aggregation and the in vitro activity of traditional Chinese medicines. Acs Chemical Biology. 10: 978-88. PMID 25606714 DOI: 10.1021/cb5009487  1
2015 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. 54: 528-37. PMID 25513739 DOI: 10.1021/bi501140k  1
2015 Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Correction: Homologous ligands accommodated by discrete conformations of a buried cavity (Proceedings of the National Academy of Sciences of the United States of America (2015) 112 (5039-5044) DOI: 10.1073/pnas.1500806112) Proceedings of the National Academy of Sciences of the United States of America. 112: E4971. DOI: 10.1073/pnas.1514835112  1
2015 Bajorath J, Jiang H, Shoichet BK, Walters WP. Computational methods for medicinal chemistry Journal of Medicinal Chemistry. 58: 1019. DOI: 10.1021/acs.jmedchem.5b00053  1
2014 London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J. Covalent docking of large libraries for the discovery of chemical probes. Nature Chemical Biology. 10: 1066-72. PMID 25344815 DOI: 10.1038/nchembio.1666  1
2014 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. Current Biology : Cb. 24: 2025-32. PMID 25155506 DOI: 10.1016/j.cub.2014.07.038  1
2014 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, et al. 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. 53: 4727-38. PMID 24955762 DOI: 10.1021/bi500595c  1
2014 Fischer M, Coleman RG, Fraser JS, Shoichet BK. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry. 6: 575-83. PMID 24950326 DOI: 10.1038/nchem.1954  1
2014 Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP. Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative. Journal of Medicinal Chemistry. 57: 5449-58. PMID 24882105 DOI: 10.1021/jm5006572  1
2014 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 Chemical Biology. 9: 1528-35. PMID 24807704 DOI: 10.1021/cb5001636  1
2014 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. Journal of Chemical Information and Modeling. 54: 1687-99. PMID 24802635 DOI: 10.1021/ci5001554  1
2014 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. Journal of the American Chemical Society. 136: 7374-82. PMID 24791931 DOI: 10.1021/ja501354q  1
2014 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, ... ... Shoichet B, et al. Large-scale identification and analysis of suppressive drug interactions. Chemistry & Biology. 21: 541-51. PMID 24704506 DOI: 10.1016/j.chembiol.2014.02.012  1
2014 Shoichet BK. Drug discovery: follow your lead. Nature Chemical Biology. 10: 244-5. PMID 24643239 DOI: 10.1038/nchembio.1484  1
2014 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 Chemical Biology. 9: 777-84. PMID 24397822 DOI: 10.1021/cb4007584  1
2013 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 Biology. 11: e1001712. PMID 24260022 DOI: 10.1371/journal.pbio.1001712  1
2013 Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. Plos One. 8: e75992. PMID 24098414 DOI: 10.1371/journal.pone.0075992  1
2013 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. 52: 6525-36. PMID 23972005 DOI: 10.1021/bi400750a  1
2013 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. Journal of the American Chemical Society. 135: 13927-33. PMID 23968233 DOI: 10.1021/ja4066078  1
2013 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. Journal of Molecular Biology. 425: 4569-83. PMID 23896298 DOI: 10.1016/j.jmb.2013.07.030  1
2013 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. Molecular Pharmacology. 84: 528-40. PMID 23887926 DOI: 10.1124/mol.113.087551  1
2013 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. 8: e69153. PMID 23874896 DOI: 10.1371/journal.pone.0069153  1
2013 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. The Journal of Biological Chemistry. 288: 19830-44. PMID 23667258 DOI: 10.1074/jbc.M112.411686  1
2013 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 β-2 adrenergic G protein coupled receptor. Acs Chemical Biology. 8: 1018-26. PMID 23485065 DOI: 10.1021/cb400103f  1
2013 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). Biochemical Pharmacology. 85: 1297-305. PMID 23473803 DOI: 10.1016/j.bcp.2013.02.026  1
2013 Merski M, Shoichet BK. The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. Journal of Medicinal Chemistry. 56: 2874-84. PMID 23473072 DOI: 10.1021/jm301823g  1
2013 Sassano MF, Doak AK, Roth BL, Shoichet BK. Colloidal aggregation causes inhibition of G protein-coupled receptors. Journal of Medicinal Chemistry. 56: 2406-14. PMID 23437772 DOI: 10.1021/jm301749y  1
2013 Lin H, Sassano MF, Roth BL, Shoichet BK. A pharmacological organization of G protein-coupled receptors. Nature Methods. 10: 140-6. PMID 23291723 DOI: 10.1038/nmeth.2324  1
2013 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. Journal of the American Chemical Society. 135: 795-803. PMID 23256477 DOI: 10.1021/ja309680b  1
2013 Shoichet BK. Drug discovery: nature's pieces. Nature Chemistry. 5: 9-10. PMID 23247169 DOI: 10.1038/nchem.1537  1
2013 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. 52: 228-38. PMID 23214420 DOI: 10.1021/bi301483z  1
2012 Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F. Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo. Proceedings of the National Academy of Sciences of the United States of America. 109: 17448-53. PMID 23043117 DOI: 10.1073/pnas.1208337109  1
2012 Merski M, Shoichet BK. Engineering a model protein cavity to catalyze the Kemp elimination. Proceedings of the National Academy of Sciences of the United States of America. 109: 16179-83. PMID 22988064 DOI: 10.1073/pnas.1208076109  1
2012 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. 486: 361-7. PMID 22722194 DOI: 10.1038/nature11159  1
2012 Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. Journal of Medicinal Chemistry. 55: 6582-94. PMID 22716043 DOI: 10.1021/jm300687e  1
2012 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 11178-83. PMID 22711801 DOI: 10.1073/pnas.1204524109  1
2012 Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK. Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. Acs Chemical Biology. 7: 1429-35. PMID 22625864 DOI: 10.1021/cb300189b  1
2012 Shoichet BK, Kobilka BK. Structure-based drug screening for G-protein-coupled receptors. Trends in Pharmacological Sciences. 33: 268-72. PMID 22503476 DOI: 10.1016/j.tips.2012.03.007  1
2012 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. Proceedings of the National Academy of Sciences of the United States of America. 109: 5517-22. PMID 22431600 DOI: 10.1073/pnas.1120431109  1
2012 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 Chemical Biology. 7: 911-9. PMID 22375814 DOI: 10.1021/cb200349v  1
2012 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. 51: 1762-73. PMID 22313111 DOI: 10.1021/bi201838b  1
2012 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. Nature Chemical Biology. 8: 144-6. PMID 22179068 DOI: 10.1038/nchembio.732  1
2011 Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. Statistical potential for modeling and ranking of protein-ligand interactions. Journal of Chemical Information and Modeling. 51: 3078-92. PMID 22014038 DOI: 10.1021/ci200377u  1
2011 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. 50: 9950-62. PMID 21999478 DOI: 10.1021/bi201312u  0.68
2011 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. Nature Chemical Biology. 7: 769-78. PMID 21926995 DOI: 10.1038/nchembio.662  1
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 15810-5. PMID 21885739 DOI: 10.1073/pnas.1106030108  1
2011 Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (London, England : 1993). 19: 1108-26. PMID 21827947 DOI: 10.1016/j.str.2011.05.012  1
2011 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. The Journal of Biological Chemistry. 286: 27718-28. PMID 21610081 DOI: 10.1074/jbc.M111.234393  1
2011 Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. Journal of the American Chemical Society. 133: 2080-3. PMID 21275375 DOI: 10.1021/ja110157u  1
2011 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, et al. The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology. 36: 638-51. PMID 21048700 DOI: 10.1038/npp.2010.195  1
2010 Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry. 49: 10267-76. PMID 21058655 DOI: 10.1021/bi101540g  1
2010 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 β-lactamase inhibitors. Journal of Medicinal Chemistry. 53: 7852-63. PMID 20945905 DOI: 10.1021/jm101015z  1
2010 Mysinger MM, Shoichet BK. Rapid context-dependent ligand desolvation in molecular docking. Journal of Chemical Information and Modeling. 50: 1561-73. PMID 20735049 DOI: 10.1021/ci100214a  1
2010 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. Journal of Medicinal Chemistry. 53: 4891-905. PMID 20540517 DOI: 10.1021/jm100488w  1
2010 Tondi D, Calò S, Shoichet BK, Costi MP. Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors. Bioorganic & Medicinal Chemistry Letters. 20: 3416-9. PMID 20452208 DOI: 10.1016/j.bmcl.2010.04.007  1
2010 Doak AK, Wille H, Prusiner SB, Shoichet BK. Colloid formation by drugs in simulated intestinal fluid. Journal of Medicinal Chemistry. 53: 4259-65. PMID 20426472 DOI: 10.1021/jm100254w  1
2010 Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA. Structure-based discovery of A2A adenosine receptor ligands. Journal of Medicinal Chemistry. 53: 3748-55. PMID 20405927 DOI: 10.1021/jm100240h  1
2010 DeGraw AJ, Keiser MJ, Ochocki JD, Shoichet BK, Distefano MD. Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs. Journal of Medicinal Chemistry. 53: 2464-71. PMID 20180535 DOI: 10.1021/jm901613f  1
2010 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. Journal of the American Chemical Society. 132: 1762-3. PMID 20088583 DOI: 10.1021/ja909817d  1
2010 Kokel D, Bryan J, Laggner C, White R, Cheung CY, Mateus R, Healey D, Kim S, Werdich AA, Haggarty SJ, Macrae CA, Shoichet B, Peterson RT. Rapid behavior-based identification of neuroactive small molecules in the zebrafish. Nature Chemical Biology. 6: 231-237. PMID 20081854 DOI: 10.1038/nchembio.307  1
2010 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. 49: 611-22. PMID 20000809 DOI: 10.1021/bi901935y  1
2010 Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in antibiotic resistance. Journal of Molecular Biology. 396: 47-59. PMID 19913034 DOI: 10.1016/j.jmb.2009.11.005  1
2010 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, et al. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. Journal of Medicinal Chemistry. 53: 52-60. PMID 19908842 DOI: 10.1021/jm901069a  1
2010 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. Journal of Medicinal Chemistry. 53: 37-51. PMID 19908840 DOI: 10.1021/jm901070c  1
2009 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, et al. Predicting new molecular targets for known drugs. Nature. 462: 175-81. PMID 19881490 DOI: 10.1038/nature08506  1
2009 Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. Molecular docking screens using comparative models of proteins. Journal of Chemical Information and Modeling. 49: 2512-27. PMID 19845314 DOI: 10.1021/ci9003706  1
2009 Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK. Crystal structures of penicillin-binding protein 6 from Escherichia coli. Journal of the American Chemical Society. 131: 14345-54. PMID 19807181 DOI: 10.1021/ja903773f  1
2009 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. Journal of Molecular Biology. 394: 747-63. PMID 19782087 DOI: 10.1016/j.jmb.2009.09.049  1
2009 Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets. Current Opinion in Biotechnology. 20: 429-36. PMID 19733475 DOI: 10.1016/j.copbio.2009.08.003  1
2009 Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y. Automated docking screens: a feasibility study. Journal of Medicinal Chemistry. 52: 5712-20. PMID 19719084 DOI: 10.1021/jm9006966  1
2009 Ferreira RS, Bryant C, Ang KK, McKerrow JH, Shoichet BK, Renslo AR. Divergent modes of enzyme inhibition in a homologous structure-activity series. Journal of Medicinal Chemistry. 52: 5005-8. PMID 19637873 DOI: 10.1021/jm9009229  1
2009 Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. Quantifying biogenic bias in screening libraries. Nature Chemical Biology. 5: 479-83. PMID 19483698 DOI: 10.1038/nchembio.180  1
2009 Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK. Docking for fragment inhibitors of AmpC beta-lactamase. Proceedings of the National Academy of Sciences of the United States of America. 106: 7455-60. PMID 19416920 DOI: 10.1073/pnas.0813029106  1
2009 Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK. Structure-based discovery of beta2-adrenergic receptor ligands. Proceedings of the National Academy of Sciences of the United States of America. 106: 6843-8. PMID 19342484 DOI: 10.1073/pnas.0812657106  1
2009 Chen Y, Shoichet BK. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nature Chemical Biology. 5: 358-64. PMID 19305397 DOI: 10.1038/nchembio.155  1
2009 Coan KE, Maltby DA, Burlingame AL, Shoichet BK. Promiscuous aggregate-based inhibitors promote enzyme unfolding. Journal of Medicinal Chemistry. 52: 2067-75. PMID 19281222 DOI: 10.1021/jm801605r  1
2009 Chen Y, McReynolds A, Shoichet BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Science : a Publication of the Protein Society. 18: 662-9. PMID 19241376 DOI: 10.1002/pro.60  1
2009 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. 48: 2237-47. PMID 19159332 DOI: 10.1021/bi802274f  1
2008 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. Journal of Molecular Biology. 384: 151-64. PMID 18822298 DOI: 10.1016/j.jmb.2008.09.009  1
2008 Huang N, Shoichet BK. Exploiting ordered waters in molecular docking. Journal of Medicinal Chemistry. 51: 4862-5. PMID 18680357 DOI: 10.1021/jm8006239  1
2008 Coan KE, Shoichet BK. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. Journal of the American Chemical Society. 130: 9606-12. PMID 18588298 DOI: 10.1021/ja802977h  1
2008 Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. Quantifying the relationships among drug classes. Journal of Chemical Information and Modeling. 48: 755-65. PMID 18335977 DOI: 10.1021/ci8000259  1
2008 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. Journal of Medicinal Chemistry. 51: 2502-11. PMID 18333608 DOI: 10.1021/jm701500e  1
2008 Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Journal of Molecular Biology. 377: 914-34. PMID 18280498 DOI: 10.1016/j.jmb.2008.01.049  1
2008 Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nature Chemical Biology. 4: 197-9. PMID 18223646 DOI: 10.1038/nchembio.65  1
2008 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. Journal of Molecular Biology. 375: 192-201. PMID 17999931 DOI: 10.1016/j.jmb.2007.10.026  1
2008 Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F. Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorganic & Medicinal Chemistry. 16: 1195-205. PMID 17997318 DOI: 10.1016/j.bmc.2007.10.075  1
2007 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. Journal of Medicinal Chemistry. 50: 5644-54. PMID 17956081 DOI: 10.1021/jm070643q  1
2007 Shoichet BK. No free energy lunch. Nature Biotechnology. 25: 1109-10. PMID 17921992 DOI: 10.1038/nbt1007-1109  1
2007 Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF. O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site. Journal of the American Chemical Society. 129: 9548-9. PMID 17628063 DOI: 10.1021/ja072370u  1
2007 Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM. Structure-based activity prediction for an enzyme of unknown function. Nature. 448: 775-9. PMID 17603473 DOI: 10.1038/nature05981  1
2007 Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology. 371: 1118-34. PMID 17599350 DOI: 10.1016/j.jmb.2007.06.002  1
2007 Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 46: 6688-95. PMID 17503785 DOI: 10.1021/bi700507d  1
2007 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. Journal of Medicinal Chemistry. 50: 2385-90. PMID 17447748 DOI: 10.1021/jm061317y  1
2007 Chen Y, Bonnet R, Shoichet BK. The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution. Journal of the American Chemical Society. 129: 5378-80. PMID 17408273 DOI: 10.1021/ja0712064  1
2007 Coan KE, Shoichet BK. Stability and equilibria of promiscuous aggregates in high protein milieus. Molecular Biosystems. 3: 208-13. PMID 17308667 DOI: 10.1039/b616314a  1
2007 Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nature Biotechnology. 25: 197-206. PMID 17287757 DOI: 10.1038/nbt1284  1
2007 Shoichet BK, Feng BY, Coan KED. Shadows on screens Rsc Biomolecular Sciences. 223-241.  1
2006 Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nature Protocols. 1: 550-3. PMID 17191086 DOI: 10.1038/nprot.2006.77  1
2006 Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. Journal of Medicinal Chemistry. 49: 6789-801. PMID 17154509 DOI: 10.1021/jm0608356  1
2006 Shoichet BK. Interpreting steep dose-response curves in early inhibitor discovery. Journal of Medicinal Chemistry. 49: 7274-7. PMID 17149857 DOI: 10.1021/jm061103g  1
2006 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. Journal of the American Chemical Society. 128: 15892-902. PMID 17147402 DOI: 10.1021/ja0658618  1
2006 Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. Predicting substrates by docking high-energy intermediates to enzyme structures. Journal of the American Chemical Society. 128: 15882-91. PMID 17147401 DOI: 10.1021/ja065860f  1
2006 Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nature Chemical Biology. 2: 720-3. PMID 17072304 DOI: 10.1038/nchembio831  1
2006 Leach AR, Shoichet BK, Peishoff CE. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. Journal of Medicinal Chemistry. 49: 5851-5. PMID 17004700 DOI: 10.1021/jm060999m  1
2006 Shoichet BK. Screening in a spirit haunted world. Drug Discovery Today. 11: 607-15. PMID 16793529 DOI: 10.1016/j.drudis.2006.05.014  1
2006 Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. Journal of Medicinal Chemistry. 49: 2151-4. PMID 16570910 DOI: 10.1021/jm060029z  1
2006 Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. Journal of the American Chemical Society. 128: 2970-6. PMID 16506777 DOI: 10.1021/ja056806m  1
2006 Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK. Probing molecular docking in a charged model binding site. Journal of Molecular Biology. 357: 1449-70. PMID 16490206 DOI: 10.1016/j.jmb.2006.01.034  1
2006 Therese Lang P, Aynechi T, Moustakas D, Shoichet B, Kuntz ID, Brooijmans N, Oshiro CM. Molecular Docking and Structure-Based Design Drug Discovery Research: New Frontiers in the Post-Genomic Era. 1-23. DOI: 10.1002/9780470131862.ch1  1
2005 Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK. High-throughput assays for promiscuous inhibitors. Nature Chemical Biology. 1: 146-8. PMID 16408018 DOI: 10.1038/nchembio718  1
2005 Brenk R, Irwin JJ, Shoichet BK. Here be dragons: docking and screening in an uncharted region of chemical space. Journal of Biomolecular Screening. 10: 667-74. PMID 16170052 DOI: 10.1177/1087057105281047  1
2005 Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry. 44: 12316-28. PMID 16156645 DOI: 10.1021/bi050801k  1
2005 Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple ligand conformations. Current Topics in Medicinal Chemistry. 5: 739-49. PMID 16101414 DOI: 10.2174/1568026054637683  1
2005 Thomas VL, Golemi-Kotra D, Kim C, Vakulenko SB, Mobashery S, Shoichet BK. Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry. 44: 9330-8. PMID 15981999 DOI: 10.1021/bi0502700  1
2005 Graves AP, Brenk R, Shoichet BK. Decoys for docking. Journal of Medicinal Chemistry. 48: 3714-28. PMID 15916423 DOI: 10.1021/jm0491187  1
2005 Tondi D, Morandi F, Bonnet R, Costi MP, Shoichet BK. Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture. Journal of the American Chemical Society. 127: 4632-9. PMID 15796528 DOI: 10.1021/ja042984o  1
2005 Irwin JJ, Shoichet BK. ZINC--a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling. 45: 177-82. PMID 15667143 DOI: 10.1021/ci049714+  1
2004 Shoichet BK. Virtual screening of chemical libraries. Nature. 432: 862-5. PMID 15602552 DOI: 10.1038/nature03197  1
2004 Ferrari AM, Wei BQ, Costantino L, Shoichet BK. Soft docking and multiple receptor conformations in virtual screening. Journal of Medicinal Chemistry. 47: 5076-84. PMID 15456251 DOI: 10.1021/jm049756p  1
2004 Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. Journal of Molecular Biology. 337: 1161-82. PMID 15046985 DOI: 10.1016/j.jmb.2004.02.015  1
2004 Horn JR, Shoichet BK. Allosteric inhibition through core disruption. Journal of Molecular Biology. 336: 1283-91. PMID 15037085 DOI: 10.1016/j.jmb.2003.12.068  1
2003 Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK. Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Biochemistry. 42: 14483-91. PMID 14661960 DOI: 10.1021/bi035054a  1
2003 Seidler J, McGovern SL, Doman TN, Shoichet BK. Identification and prediction of promiscuous aggregating inhibitors among known drugs. Journal of Medicinal Chemistry. 46: 4477-86. PMID 14521410 DOI: 10.1021/jm030191r  1
2003 McGovern SL, Helfand BT, Feng B, Shoichet BK. A specific mechanism of nonspecific inhibition. Journal of Medicinal Chemistry. 46: 4265-72. PMID 13678405 DOI: 10.1021/jm030266r  1
2003 Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S. Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. Journal of the American Chemical Society. 125: 9612-8. PMID 12904027 DOI: 10.1021/ja034861u  1
2003 Wang X, Minasov G, Blázquez J, Caselli E, Prati F, Shoichet BK. Recognition and resistance in TEM beta-lactamase. Biochemistry. 42: 8434-44. PMID 12859188 DOI: 10.1021/bi034242y  1
2003 McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. Journal of Medicinal Chemistry. 46: 2895-907. PMID 12825931 DOI: 10.1021/jm0300330  1
2003 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 Journal of Biological Chemistry. 278: 25990-25997. PMID 12676933 DOI: 10.1074/jbc.M301232200  1
2003 McGovern SL, Shoichet BK. Kinase inhibitors: not just for kinases anymore. Journal of Medicinal Chemistry. 46: 1478-83. PMID 12672248 DOI: 10.1021/jm020427b  1
2003 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. The Journal of Biological Chemistry. 278: 14092-100. PMID 12556445 DOI: 10.1074/jbc.M212690200  1
2003 Morandi F, Caselli E, Morandi S, Focia PJ, Blázquez J, Shoichet BK, Prati F. Nanomolar inhibitors of AmpC beta-lactamase. Journal of the American Chemical Society. 125: 685-95. PMID 12526668 DOI: 10.1021/ja0288338  1
2002 Beadle BM, Shoichet BK. Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrobial Agents and Chemotherapy. 46: 3978-80. PMID 12435704 DOI: 10.1128/AAC.46.12.3978-3980.2002  1
2002 Trehan I, Morandi F, Blaszczak LC, Shoichet BK. Using steric hindrance to design new inhibitors of class C beta-lactamases. Chemistry & Biology. 9: 971-80. PMID 12323371 DOI: 10.1016/S1074-5521(02)00211-9  1
2002 Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK. A model binding site for testing scoring functions in molecular docking. Journal of Molecular Biology. 322: 339-55. PMID 12217695 DOI: 10.1016/S0022-2836(02)00777-5  1
2002 Beadle BM, Shoichet BK. Structural bases of stability-function tradeoffs in enzymes. Journal of Molecular Biology. 321: 285-96. PMID 12144785 DOI: 10.1016/S0022-2836(02)00599-5  1
2002 Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking. Current Opinion in Chemical Biology. 6: 439-46. PMID 12133718 DOI: 10.1016/S1367-5931(02)00339-3  1
2002 Powers RA, Morandi F, Shoichet BK. Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure (London, England : 1993). 10: 1013-23. PMID 12121656 DOI: 10.1016/S0969-2126(02)00799-2  1
2002 Powers RA, Shoichet BK. Structure-based approach for binding site identification on AmpC beta-lactamase. Journal of Medicinal Chemistry. 45: 3222-34. PMID 12109906 DOI: 10.1021/jm020002p  1
2002 Wang X, Minasov G, Shoichet BK. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. Journal of Molecular Biology. 320: 85-95. PMID 12079336 DOI: 10.1016/S0022-2836(02)00400-X  1
2002 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. The Journal of Biological Chemistry. 277: 32149-56. PMID 12058046 DOI: 10.1074/jbc.M204212200  1
2002 Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Science : a Publication of the Protein Society. 11: 1393-408. PMID 12021438 DOI: 10.1110/ps.2830102  1
2002 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. Journal of Medicinal Chemistry. 45: 2213-21. PMID 12014959 DOI: 10.1021/jm010548w  1
2002 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 (London, England : 1993). 10: 413-24. PMID 12005439 DOI: 10.1016/S0969-2126(02)00725-6  1
2002 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. Journal of the American Chemical Society. 124: 5333-40. PMID 11996574 DOI: 10.1021/ja0259640  1
2002 McGovern SL, Caselli E, Grigorieff N, Shoichet BK. A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. Journal of Medicinal Chemistry. 45: 1712-22. PMID 11931626 DOI: 10.1021/jm010533y  1
2002 Wang X, Minasov G, Shoichet BK. Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams. Proteins. 47: 86-96. PMID 11870868 DOI: 10.1002/prot.10058  1
2002 Irwin JJ, Lorber DM, McGovern SL, Wei B, Shoichet BK. Molecular docking and drug design 2002 International Conference On Computational Nanoscience and Nanotechnology - Iccn 2002. 50-51.  1
2001 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. 40: 9207-14. PMID 11478888 DOI: 10.1021/bi0109358  1
2001 Trehan I, Beadle BM, Shoichet BK. Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site. Biochemistry. 40: 7992-9. PMID 11434768 DOI: 10.1021/bi010641m  1
2001 Tondi D, Powers RA, Caselli E, Negri MC, Blázquez J, Costi MP, Shoichet BK. Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase. Chemistry & Biology. 8: 593-611. PMID 11410378 DOI: 10.1016/S1074-5521(01)00034-5  1
2001 Beadle BM, Nicholas RA, Shoichet BK. Interaction energies between beta-lactam antibiotics and E. coli penicillin-binding protein 5 by reversible thermal denaturation. Protein Science : a Publication of the Protein Society. 10: 1254-9. PMID 11369864 DOI: 10.1110/ps.52001  1
2001 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. Chemistry & Biology. 8: 17-31. PMID 11182316 DOI: 10.1016/S1074-5521(00)00052-1  1
2001 Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins. 42: 279-93. PMID 11119652 DOI: 10.1002/1097-0134(20010201)42:2<279::AID-PROT150>3.0.CO;2-U  1
2000 Patera A, Blaszczak LC, Shoichet BK. Crystal structures of substrate and inhibitor complexes with AmpC β-lactamase: Possible implications for substrate-assisted catalysis Journal of the American Chemical Society. 122: 10504-10512. DOI: 10.1021/ja001676x  1
2000 Shoichet BK, Bussiere DE. The role of macromolecular crystallography and structure for drug discovery: Advances and caveats Current Opinion in Drug Discovery and Development. 3: 408-422.  1
1999 Powers RA, Blázquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK. The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase. Protein Science : a Publication of the Protein Society. 8: 2330-7. PMID 10595535 DOI: 10.1110/ps.8.11.2330  1
1999 Beadle BM, McGovern SL, Patera A, Shoichet BK. Functional analyses of AmpC beta-lactamase through differential stability. Protein Science : a Publication of the Protein Society. 8: 1816-24. PMID 10493583 DOI: 10.1110/ps.8.9.1816  1
1999 Shoichet BK, Leach AR, Kuntz ID. Ligand solvation in molecular docking. Proteins. 34: 4-16. PMID 10336382 DOI: 10.1002/(SICI)1097-0134(19990101)34:1<4::AID-PROT2>3.0.CO;2-6  1
1999 Tondi D, Slomczynska U, Costi MP, Watterson DM, Ghelli S, Shoichet BK. Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase. Chemistry & Biology. 6: 319-31. PMID 10322126 DOI: 10.1016/S1074-5521(99)80077-5  1
1999 Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry. 38: 2570-6. PMID 10029552 DOI: 10.1021/bi9824902  1
1999 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. 38: 1607-17. PMID 9931028 DOI: 10.1021/bi9815896  1
1998 Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ. Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design. Biochemistry. 37: 16082-92. PMID 9819201 DOI: 10.1021/bi981210f  1
1998 Weston GS, Blázquez J, Baquero F, Shoichet BK. Structure-based enhancement of boronic acid-based inhibitors of AmpC beta-lactamase. Journal of Medicinal Chemistry. 41: 4577-86. PMID 9804697 DOI: 10.1021/jm980343w  1
1998 Morosini MI, Negri MC, Shoichet B, Baquero MR, Baquero F, Blázquez J. An extended-spectrum AmpC-type β-lactamase obtained by in vitro antibiotic selection Fems Microbiology Letters. 165: 85-90. PMID 9711843 DOI: 10.1016/S0378-1097(98)00239-0  1
1998 Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Science : a Publication of the Protein Society. 7: 938-50. PMID 9568900 DOI: 10.1002/pro.5560070411  1
1997 Gassner NC, Baase WA, Lindstrom JD, Shoichet BK, Matthews BW. Isolation and characterization of multiple-methionine mutants of T4 lysozyme with simplified cores Techniques in Protein Chemistry. 8: 851-863. DOI: 10.1016/S1080-8914(97)80082-8  1
1997 Weslon GS, Shoichet BK. Structure-based inhibitor discovery of novel beta-lactamase inhibitors: potential agents for the treatment of beta-lactam-resistant infections Faseb Journal. 11: A1435.  1
1997 Tondi D, Slomczvnska U, Ghelli S, Watterson DN, Costi MP, Shoichet BK. Structure-based design and combinatorial optimization of novel thymidylate synthase inhibitors Faseb Journal. 11: A837.  1
1996 Shoichet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction. Chemistry & Biology. 3: 151-6. PMID 8807840  1
1996 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, et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nature Structural Biology. 3: 233-9. PMID 8605624  1
1995 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 Engineering. 8: 1017-22. PMID 8771182 DOI: 10.1093/protein/8.10.1017  1
1995 Shoichet BK, Baase WA, Kuroki R, Matthews BW. A relationship between protein stability and protein function. Proceedings of the National Academy of Sciences of the United States of America. 92: 452-6. PMID 7831309 DOI: 10.1073/pnas.92.2.452  1
1994 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. 33: 5623-9. PMID 8180187  1
1994 Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design Accounts of Chemical Research. 27: 117-123.  1
1993 Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science (New York, N.Y.). 259: 1445-50. PMID 8451640  1
1993 Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Engineering. 6: 723-32. PMID 7504257  1
1991 Shoichet BK, Kuntz ID. Protein docking and complementarity. Journal of Molecular Biology. 221: 327-46. PMID 1920412 DOI: 10.1016/0022-2836(91)80222-G  1
1989 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 Engineering. 3: 95-103. PMID 2594728  1
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