Published in Biochemistry on February 07, 2007
Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. Biochemistry (2012) 0.90
Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. ACS Catal (2015) 0.84
Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability. Protein Sci (2008) 0.82
Conformational diversity and enantioconvergence in potato epoxide hydrolase 1. Org Biomol Chem (2016) 0.80
Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) (2016) 0.77
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models. J Am Chem Soc (2004) 2.26
Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci U S A (2005) 1.76
A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis. Mol Cell (2007) 1.61
Free energy calculations and ligand binding. Adv Protein Chem (2003) 1.39
Absolute and relative entropies from computer simulation with applications to ligand binding. J Phys Chem B (2005) 1.36
The catalytic power of ketosteroid isomerase investigated by computer simulation. Biochemistry (2002) 1.31
Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase. Biochemistry (2007) 1.27
Resolving the energy paradox of chaperone/usher-mediated fibre assembly. Biochem J (2005) 1.25
Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem (2013) 1.16
Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB. Biochemistry (2006) 1.15
Principles of stop-codon reading on the ribosome. Nature (2010) 1.13
Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry (2006) 1.11
Probing the effect of point mutations at protein-protein interfaces with free energy calculations. Biophys J (2005) 1.09
Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem (2007) 1.07
Catalysis and linear free energy relationships in aspartic proteases. Biochemistry (2006) 1.07
Role of ribosomal protein L27 in peptidyl transfer. Biochemistry (2008) 1.03
Binding affinity prediction with different force fields: examination of the linear interaction energy method. J Comput Chem (2004) 1.02
Cold adaptation of enzyme reaction rates. Biochemistry (2008) 1.02
Bringing molecular tools into environmental resource management: untangling the molecules to policy pathway. PLoS Biol (2009) 1.01
Calculations of solute and solvent entropies from molecular dynamics simulations. Phys Chem Chem Phys (2006) 0.99
Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. J Med Chem (2008) 0.96
Energetics of activation of GTP hydrolysis on the ribosome. Nat Commun (2013) 0.96
Energetics of codon-anticodon recognition on the small ribosomal subunit. Biochemistry (2007) 0.95
Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model. Biophys J (2007) 0.95
Toward a consensus model of the HERG potassium channel. ChemMedChem (2010) 0.95
Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N --> O acyl shift reaction. J Am Chem Soc (2009) 0.95
X-ray structure of potato epoxide hydrolase sheds light on substrate specificity in plant enzymes. Protein Sci (2006) 0.94
The transition state for peptide bond formation reveals the ribosome as a water trap. Proc Natl Acad Sci U S A (2010) 0.93
Mechanism of the translation termination reaction on the ribosome. Biochemistry (2009) 0.93
Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. Biochemistry (2004) 0.93
Catalysis of potato epoxide hydrolase, StEH1. Biochem J (2005) 0.92
Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor. J Chem Inf Model (2013) 0.92
Deep eutectic solvents (DESs) are viable cosolvents for enzyme-catalyzed epoxide hydrolysis. J Biotechnol (2010) 0.92
Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods. FEBS Lett (2005) 0.91
Absolute hydration entropies of alkali metal ions from molecular dynamics simulations. J Phys Chem B (2009) 0.90
Structure-based energetics of mRNA decoding on the ribosome. Biochemistry (2014) 0.88
Force field independent metal parameters using a nonbonded dummy model. J Phys Chem B (2014) 0.87
Temperature and pH dependence of enzyme-catalyzed hydrolysis of trans-methylstyrene oxide. A unifying kinetic model for observed hysteresis, cooperativity, and regioselectivity. Biochemistry (2010) 0.87
Continuum solvation models in the linear interaction energy method. J Phys Chem B (2006) 0.87
Structure-activity relationship for extracellular block of K+ channels by tetraalkylammonium ions. FEBS Lett (2003) 0.87
Linear interaction energy: method and applications in drug design. Methods Mol Biol (2012) 0.87
Predicting binding modes from free energy calculations. J Med Chem (2008) 0.86
The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific. BMC Evol Biol (2011) 0.86
Obtaining optical purity for product diols in enzyme-catalyzed epoxide hydrolysis: contributions from changes in both enantio- and regioselectivity. Biochemistry (2012) 0.86
Implications for an ionized alkyl-enzyme intermediate during StEH1-catalyzed trans-stilbene oxide hydrolysis. Biochemistry (2006) 0.86
Modification of substrate specificity resulting in an epoxide hydrolase with shifted enantiopreference for (2,3-epoxypropyl)benzene. Chembiochem (2010) 0.86
Repertoire selection of variant single-chain Cro: toward directed DNA-binding specificity of helix-turn-helix proteins. Biochemistry (2004) 0.85
Inhibition of glutathione S-transferases by antimalarial drugs possible implications for circumventing anticancer drug resistance. Int J Cancer (2002) 0.84
Mutagenesis and homology modeling of the Tn21 integron integrase IntI1. Biochemistry (2009) 0.83
Computer simulations of structure-activity relationships for HERG channel blockers. Biochemistry (2011) 0.82
Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability. Protein Sci (2008) 0.82
Mutations in salt-bridging residues at the interface of the core and lid domains of epoxide hydrolase StEH1 affect regioselectivity, protein stability and hysteresis. Arch Biochem Biophys (2010) 0.82
Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity. J Med Chem (2004) 0.82
Role of aspartate 132 at the orifice of a proton pathway in cytochrome c oxidase. Proc Natl Acad Sci U S A (2013) 0.82
Functional validation of virtual screening for novel agents with general anesthetic action at ligand-gated ion channels. Mol Pharmacol (2013) 0.81
Computational modelling of the open-state Kv 1.5 ion channel block by bupivacaine. Biochim Biophys Acta (2003) 0.81
Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome. Chemistry (2014) 0.81
Genetic population structure of US atlantic coastal striped bass (Morone saxatilis). J Hered (2013) 0.81
Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin. Proteins (2006) 0.80
Insights into the role of Asp79(2.50) in β2 adrenergic receptor activation from molecular dynamics simulations. Biochemistry (2014) 0.80
C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions. Bioorg Med Chem (2003) 0.80
Phe369(7.38) at human 5-HT(7) receptors confers interspecies selectivity to antagonists and partial agonists. Br J Pharmacol (2009) 0.79
Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor. FEBS Lett (2006) 0.79
Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species--a case study of Pacific oysters (Crassostrea gigas). J Hered (2012) 0.78
Substrate-dependent hysteretic behavior in StEH1-catalyzed hydrolysis of styrene oxide derivatives. FEBS J (2008) 0.78
Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum. Biochemistry (2006) 0.78
Multiplexing with three-primer PCR for rapid and economical microsatellite validation. Hereditas (2014) 0.78
Computational study of the influence of solvent on (16)O/(18)O equilibrium isotope effects in phosphate deprotonation reactions. J Am Chem Soc (2002) 0.77
Does glutamine methylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors? Biochemistry (2009) 0.77
Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations. J Med Chem (2005) 0.77
Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine. J Chem Inf Model (2014) 0.77
alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases. Bioorg Med Chem (2009) 0.77
Proton uptake and pKa changes in the uncoupled Asn139Cys variant of cytochrome c oxidase. Biochemistry (2013) 0.77
The Saccharomyces cerevisiae ORF YNR064c protein has characteristics of an 'orphaned' epoxide hydrolase. Biochim Biophys Acta (2005) 0.76
Comparative analysis of putative agonist-binding modes in the human A1 adenosine receptor. Chembiochem (2004) 0.76
Substrate scope and selectivity in offspring to an enzyme subjected to directed evolution. FEBS J (2014) 0.76
Mutagenesis and computational modeling of human G-protein-coupled receptor Y2 for neuropeptide Y and peptide YY. Biochemistry (2013) 0.76
Amino acid residue 247 in canine sulphotransferase SULT1D1: a new determinant of substrate selectivity. Biochem J (2004) 0.75
Molecular dynamics study of heparin based coatings. Biomaterials (2008) 0.75
Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii. Eur J Pharm Sci (2004) 0.75
One-step enzyme extraction and immobilization for biocatalysis applications. Biotechnol J (2011) 0.75
Correction to Obtaining Optical Purity for Product Diols in Enzyme-Catalyzed Epoxide Hydrolysis: Contributions from Changes in both Enantio- and Regioselectivity. Biochemistry (2016) 0.75
Exploring the active site of tripeptidyl-peptidase II through studies of pH dependence of reaction kinetics. Biochim Biophys Acta (2012) 0.75
Isolation of novel single-chain Cro proteins targeted for binding to the bcl-2 transcription initiation site by repertoire selection and subunit combinatorics. Protein Eng Des Sel (2005) 0.75