PubRank

Brian K Shoichet

Author PubWeight™ 222.24‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005 16.75
2 Predicting new molecular targets for known drugs. Nature 2009 9.71
3 Relating protein pharmacology by ligand chemistry. Nat Biotechnol 2007 6.61
4 A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem 2002 5.67
5 Benchmarking sets for molecular docking. J Med Chem 2006 5.57
6 High-throughput assays for promiscuous inhibitors. Nat Chem Biol 2005 4.32
7 A specific mechanism of nonspecific inhibition. J Med Chem 2003 3.93
8 Large-scale prediction and testing of drug activity on side-effect targets. Nature 2012 3.88
9 Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem 2006 3.85
10 Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol 2002 3.71
11 Structure-based activity prediction for an enzyme of unknown function. Nature 2007 3.65
12 Identification and prediction of promiscuous aggregating inhibitors among known drugs. J Med Chem 2003 3.44
13 Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol 2008 2.98
14 A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem 2007 2.97
15 A model binding site for testing scoring functions in molecular docking. J Mol Biol 2002 2.94
16 Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem 2012 2.86
17 A detergent-based assay for the detection of promiscuous inhibitors. Nat Protoc 2006 2.58
18 Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A 2009 2.48
19 Deconstructing fragment-based inhibitor discovery. Nat Chem Biol 2006 2.19
20 Predicting absolute ligand binding free energies to a simple model site. J Mol Biol 2007 2.19
21 Automated docking screens: a feasibility study. J Med Chem 2009 2.14
22 Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 2002 2.10
23 Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol 2011 2.10
24 Quantifying the relationships among drug classes. J Chem Inf Model 2008 1.92
25 Structural bases of stability-function tradeoffs in enzymes. J Mol Biol 2002 1.91
26 Kinase inhibitors: not just for kinases anymore. J Med Chem 2003 1.90
27 Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol 2009 1.90
28 The Enzyme Function Initiative. Biochemistry 2011 1.87
29 Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc 2006 1.81
30 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 1.81
31 Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem 2008 1.81
32 Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem 2005 1.79
33 Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc 2008 1.74
34 Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 2004 1.73
35 Structure-based discovery of A2A adenosine receptor ligands. J Med Chem 2010 1.71
36 Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 2003 1.70
37 Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure 2002 1.70
38 Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem 2009 1.68
39 Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model 2010 1.66
40 Quantifying biogenic bias in screening libraries. Nat Chem Biol 2009 1.66
41 A pharmacological organization of G protein-coupled receptors. Nat Methods 2013 1.65
42 Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci 2002 1.61
43 Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol 2009 1.60
44 Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol 2008 1.57
45 Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem 2010 1.54
46 Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Structure 2002 1.54
47 Soft docking and multiple receptor conformations in virtual screening. J Med Chem 2004 1.47
48 Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol 2009 1.47
49 Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry 2009 1.47
50 In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol 2013 1.47
51 Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry 2005 1.46
52 Structure-based approach for binding site identification on AmpC beta-lactamase. J Med Chem 2002 1.45
53 Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem 2010 1.45
54 Decoys for docking. J Med Chem 2005 1.43
55 Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J Biol Chem 2003 1.43
56 Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem 2006 1.42
57 Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc 2003 1.41
58 Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother 2002 1.39
59 Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst 2007 1.38
60 Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol 2011 1.37
61 Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A 2012 1.36
62 Molecular docking screens using comparative models of proteins. J Chem Inf Model 2009 1.36
63 Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry 2005 1.32
64 The chemical basis of pharmacology. Biochemistry 2010 1.30
65 Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A 2011 1.29
66 Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams. Proteins 2002 1.27
67 Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. Proc Natl Acad Sci U S A 2012 1.25
68 Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol 2007 1.22
69 Probing molecular docking in a charged model binding site. J Mol Biol 2006 1.17
70 Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. ACS Chem Biol 2012 1.17
71 The structural bases of antibiotic resistance in the clinically derived mutant beta-lactamases TEM-30, TEM-32, and TEM-34. J Biol Chem 2002 1.16
72 The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc 2006 1.16
73 Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem 2013 1.16
74 Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol 2009 1.16
75 Allosteric inhibition through core disruption. J Mol Biol 2004 1.14
76 Colloidal aggregation causes inhibition of G protein-coupled receptors. J Med Chem 2013 1.13
77 Docking for fragment inhibitors of AmpC beta-lactamase. Proc Natl Acad Sci U S A 2009 1.13
78 The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology 2010 1.09
79 Resolution of chiral phosphate, phosphonate, and phosphinate esters by an enantioselective enzyme library. J Am Chem Soc 2006 1.08
80 Exploiting ordered waters in molecular docking. J Med Chem 2008 1.07
81 Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol 2013 1.05
82 Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc 2009 1.05
83 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 2005 1.05
84 Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase. J Mol Biol 2008 1.05
85 Colloid formation by drugs in simulated intestinal fluid. J Med Chem 2010 1.04
86 Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem 2010 1.04
87 The hunt for 8-oxoguanine deaminase. J Am Chem Soc 2010 1.04
88 Colloidal drug formulations can explain "bell-shaped" concentration-response curves. ACS Chem Biol 2014 1.04
89 Recognition and resistance in TEM beta-lactamase. Biochemistry 2003 1.03
90 Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol 2013 1.01
91 Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo. Proc Natl Acad Sci U S A 2012 1.00
92 Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc 2011 1.00
93 The acylation mechanism of CTX-M beta-lactamase at 0.88 a resolution. J Am Chem Soc 2007 1.00
94 Ligand pose and orientational sampling in molecular docking. PLoS One 2013 0.99
95 Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors. Bioorg Med Chem 2007 0.96
96 Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry 2007 0.96
97 Prediction and evaluation of protein farnesyltransferase inhibition by commercial drugs. J Med Chem 2010 0.96
98 Divergent modes of enzyme inhibition in a homologous structure-activity series. J Med Chem 2009 0.96
99 Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model 2011 0.95
100 Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. J Am Chem Soc 2003 0.95
101 Engineering a model protein cavity to catalyze the Kemp elimination. Proc Natl Acad Sci U S A 2012 0.95
102 Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen 2005 0.94
103 O-aryloxycarbonyl hydroxamates: new beta-lactamase inhibitors that cross-link the active site. J Am Chem Soc 2007 0.93
104 Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Biochemistry 2003 0.93
105 Design, synthesis, crystal structures, and antimicrobial activity of sulfonamide boronic acids as β-lactamase inhibitors. J Med Chem 2010 0.91
106 A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase. J Biol Chem 2003 0.91
107 Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc 2013 0.90
108 Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Sci 2009 0.89
109 Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily. Biochemistry 2012 0.88
110 Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities. PLoS One 2013 0.88
111 Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. Biochemistry 2012 0.88
112 Muscarinic receptors as model targets and antitargets for structure-based ligand discovery. Mol Pharmacol 2013 0.87
113 A chemical screen identifies class a g-protein coupled receptors as regulators of cilia. ACS Chem Biol 2012 0.87
114 Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase . Biochemistry 2010 0.87
115 Using steric hindrance to design new inhibitors of class C beta-lactamases. Chem Biol 2002 0.87
116 A survey of antiprion compounds reveals the prevalence of non-PrP molecular targets. J Biol Chem 2011 0.86
117 Substrate deconstruction and the nonadditivity of enzyme recognition. J Am Chem Soc 2014 0.83
118 The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. J Med Chem 2013 0.82
119 Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy. J Med Chem 2007 0.82
120 Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors. Bioorg Med Chem Lett 2010 0.82
121 Structure-guided discovery of new deaminase enzymes. J Am Chem Soc 2013 0.80
122 Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). Biochem Pharmacol 2013 0.79
123 Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 2014 0.79
124 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 0.78
125 Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol 2014 0.78
126 Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative. J Med Chem 2014 0.77
127 Drug discovery: nature's pieces. Nat Chem 2013 0.76
128 Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2015 0.76
129 Erratum: Covalent docking of large libraries for the discovery of chemical probes. Nat Chem Biol 2015 0.75
130 Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry 2013 0.75
131 Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry 2015 0.75
132 Structure-based design and discovery of new M2 receptor agonists. J Med Chem 2017 0.75
133 Advances in Computational Medicinal Chemistry: A Reflection on the Evolution of the Field and Perspective Going Forward. J Med Chem 2016 0.75