Shoichet Laboratory

Publications


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 (7), e69153 (2013). [Pubmed | DOI]
  • 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 288 (27), 19830-44 (2013). [Pubmed | DOI]
  • 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 85 (9), 1297-305 (2013). [Pubmed | DOI]
  • Fan H, Hitchcock DS, Seidel RD 2nd, 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 135 (2), 795-803 (2013). [Pubmed | DOI]
  • Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky YV, Hillerich B, Seidel RD, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes.. Biochemistry Epub ahead, (2013). [Pubmed]
  • Hitchcock DS, Fan H, Kim J, Vetting MW, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. Structure-Guided Discovery of New Deaminase Enzymes.. J Am Chem Soc Epub ahead, (2013). [Pubmed]
  • 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 forStructure-Based Ligand Discovery.. Mol Pharmacol Epub ahead (in press), xxx (2013). [Pubmed]
  • Lin H, Sassano MF, Roth BL, Shoichet BK. A pharmacological organization of G protein-coupled receptors. Nat Methods 10 (2), 140-6 (2013). [Pubmed | DOI]
  • Merski M, Shoichet BK. The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. J Med Chem 56 (7), 2874-84 (2013). [Pubmed | DOI]
  • 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 (1), 228-38 (2013). [Pubmed | DOI]
  • 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 425 (22), 4569-83 (2013). [Pubmed | DOI | Access the recommendation on F1000Prime">]
  • Sassano MF, Doak AK, Roth BL, Shoichet BK. Colloidal aggregation causes inhibition of G protein-coupled receptors. J Med Chem 56 (6), 2406-14 (2013). [Pubmed | DOI]
  • Shoichet BK. Drug discovery: nature's pieces. Nat Chem 5 (1), 9-10 (2013). [Pubmed | DOI]
  • 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 ?-2 adrenergic G protein coupled receptor.. ACS Chem Biol 8 (5), 1018-26 (2013). [Pubmed | DOI]

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 Chem Biol (epub), (2012). [Pubmed | DOI]
  • Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F. Fragment-guided design of subnanomolar ?-lactamase inhibitors active in vivo. Proc Natl Acad Sci U S A 109 (43), 17448-53 (2012). [Pubmed | DOI]
  • Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CYJ, Minor DL, Roth BL, Peterson RT, Shoichet BK. chemical informatics and target identification in a zebrafish phenotypic screen. Nature Chemical Biology 8 (2), 144-146 (2012). [Pubmed | DOI]
  • Merski M, Shoichet BK. Engineering a model protein cavity to catalyze the Kemp elimination. Proc Natl Acad Sci U S A 109 (40), 16179-83 (2012). [Pubmed | DOI]
  • 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 26 (55), 6582-94 (2012). [Pubmed | DOI]
  • 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 55 (14), 6582-94 (2012). [Pubmed | DOI]
  • 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 109 (14), 5517-22 (2012). [Pubmed | DOI]
  • Shoichet BK, Kobilka BK. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci. (epub), (2012). [Pubmed | DOI | Science Direct]
  • 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 (8), 1762-73 (2012). [Pubmed | DOI]

2011
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  • 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 (11), 769-778 (2011). [Pubmed | DOI | NRDD Highlight | F1000 Evaluation | Download PDF]

  • 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 (12), 3078-3092 (2011). [Pubmed | DOI]
  • 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 133 (7), 2080-3 (2011). [Pubmed | DOI | Download PDF]
  • 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 target. J Biol Chem 286 (31), 27718-28 (2011). [Pubmed | DOI | JBC Full Text | Download PDF]
  • 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. PNAS 108 (38), (2011). [Pubmed | DOI | Download PDF]

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 (9), 3748-55 (2010). [Pubmed | DOI | Download PDF]
  • 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 (3), 611-22 (2010). [Pubmed | DOI | Download PDF]
  • 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 (6), 2464-71 (2010). [Pubmed | DOI | Download PDF]
  • Doak AK, Wille H, Prusiner SB, Shoichet BK. Colloid Formation by Drugs in Simulated Intestinal Fluid. J. Med. Chem. 53 (10), 4259-4265 (2010). [Pubmed | DOI | Download PDF]
  • 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 Beta-Lactamase Inhibitors.. Journal of Medicinal Chemistry , (2010). [Pubmed | DOI | Download PDF]
  • 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 (13), 4891-905 (2010). [Pubmed | DOI | Download PDF]
  • 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 , (2010). [Pubmed | DOI | Download PDF]
  • 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 (1), 37-51 (2010). [Pubmed | DOI | Download PDF]
  • Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry 49 (48), 10267-76 (2010). [Pubmed | DOI | Download PDF]
  • 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 , (2010). [Pubmed | DOI | Download PDF]
  • 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.. Journal of Medicinal Chemistry 53 (1), 52-60 (2010). [Pubmed | DOI | Download PDF]
  • Mysinger MM, Shoichet BK. Rapid context-dependent ligand desolvation in molecular docking. Journal of Chemical Information and Modeling 50 (9), 1561-73 (2010). [Pubmed | DOI | HTML | Download PDF]
  • Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in antibiotic resistance.. Journal of Molecular Biology 396 (1), 47-59 (2010). [Pubmed | DOI | Download PDF]
  • 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 36 (3), 638-51 (2010). [Pubmed | DOI | Download PDF]

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 , (2009). [Pubmed | DOI | Download PDF]
  • Chen Y, McReynolds A, Shoichet BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis.. Protein Sci 18 (3), 662-9 (2009). [Pubmed | DOI | Download PDF]
  • Chen Y, Shoichet BK. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nature Chemical Biology 5 (5), 358-364 (2009). [Pubmed | DOI | News and Views | Download PDF]
  • 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 (40), 14345-54 (2009). [Pubmed | DOI | Download PDF]
  • Coan KE, Maltby DA, Burlingame AL, Shoichet BK. Promiscuous Aggregate-Based Inhibitors Promote Enzyme Unfolding.. J Med Chem 52 (7), 2067-2075 (2009). [Pubmed | DOI | Faculty of 1000 | Download PDF]
  • 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 (18), 5712-20 (2009). [Pubmed | DOI | Download PDF]
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  • Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets.. Current opinion in biotechnology 20 (4), 429-36 (2009). [Pubmed | DOI | Download PDF]
  • Kolb P, Irwin JJ. Docking screens: right for the right reasons?. Current Topics in Medicinal Chemistry 9 (9), 755-70 (2009). [Pubmed]
  • Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK. Structure-based discovery of beta2-adrenergic receptor ligands. PNAS 106 (16), 6843-6848 (2009). [Pubmed | DOI | Download PDF]
  • Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK. Docking for fragment inhibitors of AmpC beta-lactamase. PNAS 106 (18), 7455-60 (2009). [Pubmed | DOI | Download PDF]
  • Xiang D, Kolb P, Fedorov A, Meier M, Fedorov E, Nguyen T, Sterner R, Almo S, Shoichet B, Raushel F. Functional Annotation and Three-Dimensional Structure of Dr0930 from Deinococcus radiodurans, a Close Relative of Phosphotriesterase in the Amidohydrolase Superfamily. Biochemistry 48 (10), 2237-2247 (2009). [Pubmed | DOI | Download PDF]

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. J Med Chem 51 (8), 2502-11 (2008). [Pubmed | DOI | Download PDF]
  • Coan KE, Shoichet BK. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc 130 (29), 9606-12 (2008). [Pubmed | DOI | Download PDF]
  • 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 375 (1), 192-201 (2008). [Pubmed | DOI | Download PDF]
  • Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol 377 (3), 914-34 (2008). [Pubmed | DOI | Download PDF]
  • Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. Quantifying the Relationships among Drug Classes. J Chem Inf Model 48 (4), 755-765 (2008). [Pubmed | DOI | Download PDF]
  • Huang N, Shoichet BK. Exploiting ordered waters in molecular docking. J Med Chem 51 (16), 4862-5 (2008). [Pubmed | DOI | Download PDF]
  • Morandi S, Morandi F, Caselli E, Shoichet BK, Prati F. Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorg Med Chem 16 (3), 1195-205 (2008). [Pubmed | DOI | Download PDF]

2007

  • Chen Y, Bonnet R, Shoichet BK. The Acylation Mechanism of CTX-M beta-Lactamase at 0.88 A Resolution. J Am Chem Soc 129 (17), 5378-5380 (2007). [Pubmed | DOI | Download PDF]
  • Coan KE, Shoichet BK. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst 3 (3), 208-13 (2007). [Pubmed | DOI | Download PDF]
  • 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 50 (10), 2385-2390 (2007). [Pubmed | DOI | Download screening results | Download PDF]
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  • 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 (7155), 775-9 (2007). [Pubmed | DOI | Download PDF]
  • Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007). [Pubmed | DOI | Download PDF]
  • 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 371 (4), 1118-1134 (2007). [Pubmed | DOI | Download PDF]
  • Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for Function Trade-Offs in the Enolase Superfamily 'Catalytic Module'. Biochemistry 46 (23), 6688-95 (2007). [Pubmed | DOI | Download PDF]
  • 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 50 (23), 5644-54 (2007). [Pubmed | DOI | Download PDF]
  • 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 129 (31), 9548-9 (2007). [Pubmed | DOI | Download PDF]

2006

  • Babaoglu K, Shoichet BK. Deconstructing fragment-based inhibitor discovery. Nat Chem Biol 2 (12), 720-3 (2006). [Pubmed | DOI | Download PDF]
  • Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK. Probing molecular docking in a charged model binding site. J Mol Biol 357 (5), 1449-70 (2006). [Pubmed | DOI | Download PDF]
  • Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc 128 (9), 2970-6 (2006). [Pubmed | DOI | Download PDF]
  • Feng BY, Shoichet BK. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem 49 (7), 2151-4 (2006). [Pubmed | DOI | Download PDF]
  • Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nature Protocols 1, 550-3 (2006). [Pubmed | DOI | Download PDF]
  • 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 128 (49), 15882-891 (2006). [Pubmed | DOI | Download PDF]
  • Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 49 (23), 6789-801 (2006). [Pubmed | DOI | Download PDF]
  • Leach AR, Shoichet BK, Peishoff CE. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem 49 (20), 5851-5 (2006). [Pubmed | DOI | Download PDF]
  • 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 128 (49), 15892-902 (2006). [Pubmed | DOI | Download PDF]
  • Shoichet BK. Screening in a spirit haunted world. Drug Discov Today 11 (13-14), 607-15 (2006). [Pubmed | DOI | Download PDF]
  • Shoichet BK. Interpreting Steep Dose-Response Curves in Early Inhibitor Discovery. J Med Chem 49 (25), 7274-7277 (2006). [Pubmed | DOI | Download PDF]

2005
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  • Brenk R, Irwin JJ, Shoichet BK. Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen 10 (7), 667-74 (2005). [Pubmed | DOI | Download PDF]

  • Chen Y, Delmas J, Sirot J, Shoichet B, Bonnet R. Atomic Resolution Structures of CTX-M beta-Lactamases: Extended Spectrum Acti vities from Increased Mobility and Decreased Stability. J Mol Biol 348 (2), 349-62 (2005). [Pubmed | DOI | PDB 1YLT | PDB 1YLJ | PDB 1YLP | PDB 1YLW | Download PDF]
  • Chen Y, Shoichet B, Bonnet R. Structure, function, and inhibition along the reaction coordinate of CTX-M beta-lactamases. J Am Chem Soc 127 (15), 5423-34 (2005). [Pubmed | DOI | Download PDF]
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  • Feng BY, Shelat A, Doman TN, Guy RK, Shoichet BK. High-throughput assays for promiscuous inhibitors. Nature Chem Biol 1 (3), 146-8 (2005). [Pubmed | DOI | Download PDF]
  • Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry 44 (37), 12316-28 (2005). [Pubmed | DOI | Download PDF]
  • Irwin JJ, Shoichet BK. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J Chem Inf Model 45 (1), 177-82 (2005). [Pubmed | DOI | Supporting Info | Download PDF]
  • Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem 5 (8), 739-49 (2005). [Pubmed | Download PDF]
  • 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 ( 26), 9330-9338 (2005). [Pubmed | DOI | Download PDF]
  • 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. J Am Chem Soc 127 (13), 5423-34 (2005). [Pubmed | DOI | PDB 1XGJ | PDB 1XGI | Download PDF]

2004

  • Ferrari AM, Wei BQ, Costantino L, Shoichet BK. Soft Docking and Multiple Receptor Conformations in Virtual Screening. J Med Chem 47 (21), 5076 -84 (2004). [Pubmed | DOI | Download PDF]
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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. J Biol Chem 278 (16), 14092-100 (2003). [Pubmed | DOI | Faculty of 1000 | Download PDF]
  • McGovern SL, Helfand BT, Feng B, Shoichet BK. A Specific Mechanism of Nonspecific Inhibition. J Med Chem 46 (20), 4265-72 (2003). [Pubmed | DOI | Download PDF]
  • McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 46 (14), 2895-907 (2003). [Pubmed | DOI | Supporting Info | Download PDF]
  • 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 125 (32), 9612-8 (2003). [Pubmed | DOI | Download PDF]
  • Morandi F, Caselli E, Morandi S, Focia PJ, Blazquez J, Shoichet BK, Prati F. Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc 125 (3), 685-95 (2003). [Pubmed | DOI | PDB 1MXO | PDB 1MY8 | News In Brief]
  • Roth TA, Minasov G, Morandi S, Prati F, Shoichet BK. Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Biochemistry 42 (49), 14483-91 (2003). [Pubmed | DOI | Download PDF]
  • 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 278 (28), 25990-7 (2003). [Pubmed | DOI | Download PDF]
  • Wang X, Minasov G, Blazquez J, Caselli E, Prati F, Shoichet BK. Recognition and resistance in TEM beta-lactamase. Biochemistry 42 (28), 8434-44 (2003). [Pubmed | DOI | Download PDF]

2002

  • Beadle BM, Shoichet BK. Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother 46 (12), 3978-80 (2002). [Pubmed | DOI | PDB 1LL5 | Download PDF]
  • 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 (Camb) 10 (3), 413-24 (2002). [Pubmed | DOI | Erratum | Download PDF]
  • 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 45 (11), 2213-21 (2002). [Pubmed | DOI | NRDD Highlight | Faculty of 1000 | Download PDF]
  • Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Science 11, 1393-1408 (2002). [Pubmed | DOI | Supplemental Data | Download PDF]
  • Minasov G, Wang X, Shoichet BK. An ultrahigh resolution structure of TEM-1 -lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc 124 (19), 5333-40 (2002). [Pubmed | DOI | PDB 1M40 | Download PDF]
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  • Powers RA, Morandi F, Shoichet BK. Structure-based discovery of a novel, non-covalent inhibitor of AmpC -lactamase. Structure 10 (7), 1013-23 (2002). [Pubmed | DOI | PDB 1L2S | Download PDF]
  • Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking (Review). Current Opinion in Chemical Biology 6, 439-46 (2002). [Pubmed | DOI | Download PDF]
  • Trehan I, Morandi F, Blaszczak LC, Shoichet BK. Using steric hindrance to design new inhibitors of class C -lactamases. Chem Biol 9 (9), 971-80 (2002). [Pubmed | DOI | PDB 1LL9 | PDB 1LLB | Download PDF]
  • Wang X, Minasov G, Shoichet BK. The structural bases of antibiotic resistance in the clinically-derived mutant -lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem 277 (35), 32149-56 (2002). [Pubmed | DOI | PDB 1LHY | PDB 1LI0 | PDB 1LI9 | Download PDF]
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  • Wang X, Minasov G, Shoichet BK. Non-covalent interaction energies in covalent complexes: TEM-1 -lactamase and -lactams. Proteins 47 (1), 86-96 (2002). [Pubmed | DOI | PDB 1JVJ | Download PDF]

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 Sci 10 (6), 1254-9 (2001). [Pubmed | DOI]
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  • 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 8 (1), 17-31 (2001). [Pubmed | DOI | PDB 1FSW | PDB 1FSY]
  • 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 (31), 9207-14 (2001). [Pubmed | DOI | PDB 1IEL | PDB 1IEM]
  • Su AI, Lorber DM, Weston GS, Baase WA, Matthew 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 (2001). [Pubmed | DOI | Supplementary Material]
  • Tondi D, Powers RA, Caselli E, Negri M, Blazquez J, Costi MP, Shoichet BK. Structure-based design and in-parallel synthesis of inhibitors of AmpC -lactamases. Chem Biol 8 (6), 593-611 (2001). [Pubmed | DOI | PDB 1GA9]
  • Trehan I, Beadle BM, Shoichet BK. Inhibition of AmpC -lactamase through a destabilizing interaction in the active site. Biochemistry 40 (27), 7992-9 (2001). [Pubmed | DOI | PDB 1I5Q]

2000

  • Patera A, Blaszczak LC, Shoichet BK. Crystal structures of substrate and inhibitor complexes with AmpC -lactamase: possible implications for substrate-assisted catalysis. J Am Chem Soc 122 (43), 10504-12 (2000). [DOI | PDB 1FCM | PDB 1FCN | PDB 1FCO]
  • Shoichet BK, Bussiere DE. Macromolecular crystallography and lead discovery: possibilities and limitations (Review). Current Opinion in Drug Discovery & Development 3, 408-22 (2000).

1999

  • Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK. Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry 38, 2570-2576 (1999). [Pubmed | DOI]
  • Beadle BM, McGovern SL, Patera A, Shoichet BK. Functional analyses of AmpC -lactamase through differential stability. Protein Sci 8 (9), 1816-24 (1999). [Pubmed]
  • Powers RA, Blazquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK. The complexed structure and antimicrobial activity of a non-β-lactam inhibitor of AmpC β-lactamase. Protein Science 8, 2330-2337 (1999). [Pubmed | DOI]
  • Shoichet BK, Leach AR, Kuntz ID. Ligand solvation in molecular docking. Proteins 34, 4-16 (1999). [Pubmed | DOI]
  • 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, 1607-1617 (1999). [Pubmed | DOI | PDB 1TSL]
  • 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. Chem Biol 6 (5), 319-31 (1999). [Pubmed | DOI]

1998

  • Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Science 7, 938-950 (1998). [Pubmed | DOI]
  • Morosini MI, Negri MC, Shoichet B, Baquero MR, Baquero F, Blazquez J. An extended-spectrum AmpC-type β-lactamase obtained by in vitro antibiotic selection. FEMS Microbiology Letters 165, 85-90 (1998). [Pubmed | DOI]
  • Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ. Three-dimensional structure of AmpC β-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design. Biochemistry 37, 16082-1609 (1998). [Pubmed | DOI | PDB 2BLS]
  • Weston GS, Blazquez J, Baquero F, Shoichet BK. Structure-based enhancement of boronic acid-based inhibitors of AmpC β-lactamase. Journal of Medicinal Chemistry 41, 4577-4586 (1998). [Pubmed | DOI]

1997

  • Shoichet BK. Receptor Preorganization for Activity and its Role in Identifying Ligand-Binding Sites on Proteins. In Practical Application of Computer-Aided Drug Design (ed. Charifson PS), pp. 195-226 (Marcel Dekker Inc, New York, 1997).

1996

  • Shoichet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction (Review). Chemistry & Biology 3, 151-6 (1996). [Pubmed]
  • 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 β-lactamase inhibitory protein to TEM-1 β-lactamase. Nature Structural Biology 3, 233-239 (1996). [Pubmed | DOI]

1995

  • Shoichet BK, Baase WA, Kuroki R, Matthews BW. A relationship between protein stability and protein function. Proc Natl Acad Sci U S A 92 (2), 452-6 (1995). [Pubmed | PDF | PDB 253L | PDB 254L | PDB 255L]
  • 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, 1017-1022 (1995). [Pubmed | DOI]

1994

  • Kuntz ID, Meng EC, Shoichet BK. Structure-based molecular design. Accounts of Chemical Research 27, 117-123 (1994). [DOI]
  • 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, 5623-5629 (1994). [Pubmed | DOI]

1993

  • Shoichet BK, Kuntz ID. Matching chemistry and shape in molecular docking. Protein Engineering 6, 723-732 (1993). [Pubmed | DOI]
  • Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. Structure-based discovery of inhibitors of thymidylate synthase. Science 259, 1445-1450 (1993). [Pubmed | DOI]

1992

  • Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992). [DOI]
  • Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992). [DOI | Download PDF]

1991

  • Shoichet BK, Kuntz ID. Protein docking and complementarity. Journal of Molecular Biology 221, 327-346 (1991). [Pubmed | DOI]

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 (1989). [Pubmed | DOI]