Published in Biochemistry on May 16, 2007
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol (2009) 1.36
Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat Commun (2012) 1.16
Experimental support for the foldability-function tradeoff hypothesis: segregation of the folding nucleus and functional regions in fibroblast growth factor-1. Protein Sci (2012) 1.13
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol (2008) 0.98
A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity. PLoS One (2012) 0.89
Rational design, preparation, and characterization of a therapeutic enzyme mutant with improved stability and function for cocaine detoxification. ACS Chem Biol (2014) 0.84
Apparent tradeoff of higher activity in MMP-12 for enhanced stability and flexibility in MMP-3. Biophys J (2010) 0.83
The organization of domains in proteins obeys Menzerath-Altmann's law of language. BMC Syst Biol (2015) 0.83
The contribution of coevolving residues to the stability of KDO8P synthase. PLoS One (2011) 0.82
The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins (2011) 0.79
Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis. BMC Bioinformatics (2012) 0.76
Circumventing the stability-function trade-off in an engineered FN3 domain. Protein Eng Des Sel (2016) 0.75
ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model (2005) 16.75
Predicting new molecular targets for known drugs. Nature (2009) 9.71
Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat (2002) 9.48
Relating protein pharmacology by ligand chemistry. Nat Biotechnol (2007) 6.61
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A (2002) 6.00
A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J Med Chem (2002) 5.67
Benchmarking sets for molecular docking. J Med Chem (2006) 5.57
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res (2003) 4.83
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol (2009) 4.76
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
High-throughput assays for promiscuous inhibitors. Nat Chem Biol (2005) 4.32
A specific mechanism of nonspecific inhibition. J Med Chem (2003) 3.93
Large-scale prediction and testing of drug activity on side-effect targets. Nature (2012) 3.88
Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem (2006) 3.85
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. J Mol Biol (2002) 3.71
Structure-based activity prediction for an enzyme of unknown function. Nature (2007) 3.65
Identification and prediction of promiscuous aggregating inhibitors among known drugs. J Med Chem (2003) 3.44
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res (2006) 3.40
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol (2008) 2.98
A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem (2007) 2.97
A model binding site for testing scoring functions in molecular docking. J Mol Biol (2002) 2.94
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem (2012) 2.86
Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry (2006) 2.65
A detergent-based assay for the detection of promiscuous inhibitors. Nat Protoc (2006) 2.58
Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A (2009) 2.48
Evolution of enzyme superfamilies. Curr Opin Chem Biol (2006) 2.30
Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol (2007) 2.29
Predicting absolute ligand binding free energies to a simple model site. J Mol Biol (2007) 2.19
Deconstructing fragment-based inhibitor discovery. Nat Chem Biol (2006) 2.19
Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys (2005) 2.18
Automated docking screens: a feasibility study. J Med Chem (2009) 2.14
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem (2002) 2.10
Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol (2011) 2.10
Quantifying the relationships among drug classes. J Chem Inf Model (2008) 1.92
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure (2008) 1.91
Structural bases of stability-function tradeoffs in enzymes. J Mol Biol (2002) 1.91
Kinase inhibitors: not just for kinases anymore. J Med Chem (2003) 1.90
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol (2009) 1.90
The Enzyme Function Initiative. Biochemistry (2011) 1.87
Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc (2006) 1.81
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
Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J Med Chem (2008) 1.81
Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem (2005) 1.79
Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc (2008) 1.74
Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol (2004) 1.73
Structure-based discovery of A2A adenosine receptor ligands. J Med Chem (2010) 1.71
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem (2003) 1.70
Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure (2002) 1.70
Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem (2009) 1.68
Rapid context-dependent ligand desolvation in molecular docking. J Chem Inf Model (2010) 1.66
Quantifying biogenic bias in screening libraries. Nat Chem Biol (2009) 1.66
A pharmacological organization of G protein-coupled receptors. Nat Methods (2013) 1.65
Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci (2002) 1.61
Automated discovery of 3D motifs for protein function annotation. Bioinformatics (2006) 1.60
Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol (2009) 1.60
Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J Mol Biol (2008) 1.57
Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors. J Med Chem (2010) 1.54
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
A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biol (2006) 1.52
The Structure-Function Linkage Database. Nucleic Acids Res (2013) 1.50
Soft docking and multiple receptor conformations in virtual screening. J Med Chem (2004) 1.47
Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol (2009) 1.47
In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol (2013) 1.47
Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry (2009) 1.47
Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry (2004) 1.47
Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature (2013) 1.46
Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry (2005) 1.46
Structure-based approach for binding site identification on AmpC beta-lactamase. J Med Chem (2002) 1.45
Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution. Proteins (2002) 1.45
Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem (2010) 1.45
Decoys for docking. J Med Chem (2005) 1.43
Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J Biol Chem (2003) 1.43
Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J Med Chem (2006) 1.42
Nanomolar inhibitors of AmpC beta-lactamase. J Am Chem Soc (2003) 1.41
Divergent evolution in enolase superfamily: strategies for assigning functions. J Biol Chem (2011) 1.40
Structural basis for imipenem inhibition of class C beta-lactamases. Antimicrob Agents Chemother (2002) 1.39
Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst (2007) 1.38
Chemical informatics and target identification in a zebrafish phenotypic screen. Nat Chem Biol (2011) 1.37
Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily. Biochemistry (2003) 1.36
Identifying mechanism-of-action targets for drugs and probes. Proc Natl Acad Sci U S A (2012) 1.36
Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol (2009) 1.36
Molecular docking screens using comparative models of proteins. J Chem Inf Model (2009) 1.36
Novel non-peptidic vinylsulfones targeting the S2 and S3 subsites of parasite cysteine proteases. Bioorg Med Chem Lett (2009) 1.33
Structural consequences of the inhibitor-resistant Ser130Gly substitution in TEM beta-lactamase. Biochemistry (2005) 1.32
Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol (2006) 1.31
The chemical basis of pharmacology. Biochemistry (2010) 1.30
Glutathione transferases are structural and functional outliers in the thioredoxin fold. Biochemistry (2009) 1.30
Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A (2011) 1.29
Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams. Proteins (2002) 1.27
An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations. PLoS Comput Biol (2009) 1.26
Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. Proc Natl Acad Sci U S A (2012) 1.25
Differential use of protease families for invasion by schistosome cercariae. Biochimie (2007) 1.24
Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci (2009) 1.23
Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol (2007) 1.22
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature (2013) 1.22
At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. Biochemistry (2008) 1.22
Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput (2005) 1.19
Structural and functional relationships in the virulence-associated cathepsin L proteases of the parasitic liver fluke, Fasciola hepatica. J Biol Chem (2007) 1.19