Published in J Phys Chem B on April 07, 2005
Computational model for nanocarrier binding to endothelium validated using in vivo, in vitro, and atomic force microscopy experiments. Proc Natl Acad Sci U S A (2010) 1.53
Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions. Proteins (2010) 1.45
Molecular mechanism of ion-ion and ion-substrate coupling in the Na+-dependent leucine transporter LeuT. Biophys J (2008) 1.34
Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U S A (2007) 1.26
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
Multivalent binding of nanocarrier to endothelial cells under shear flow. Biophys J (2011) 1.13
Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys (2011) 1.12
Multiscale Modeling of Functionalized Nanocarriers in Targeted Drug Delivery. Curr Nanosci (2011) 1.04
A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes. Proteins (2010) 1.02
The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophys J (2005) 1.01
Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding. Curr Protein Pept Sci (2009) 0.95
Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations. J Chem Phys (2009) 0.94
Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties. J Chem Theory Comput (2009) 0.94
Towards an integrated proteomic and glycomic approach to finding cancer biomarkers. Genome Med (2009) 0.94
Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics. J Mol Recognit (2010) 0.91
Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3. J Biomol NMR (2009) 0.90
Free energy simulations of ligand binding to the aspartate transporter Glt(Ph). Biophys J (2011) 0.90
Calculations of protein-ligand binding entropy of relative and overall molecular motions. J Comput Aided Mol Des (2007) 0.88
Fatty acid binding proteins: same structure but different binding mechanisms? Molecular dynamics simulations of intestinal fatty acid binding protein. Biophys J (2005) 0.86
Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition. Br J Pharmacol (2009) 0.85
Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects. J Phys Chem B (2009) 0.84
Investigation of atomic level patterns in protein--small ligand interactions. PLoS One (2009) 0.83
Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. J Chem Theory Comput (2013) 0.82
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding. Biophys J (2006) 0.80
Molecular dynamics simulations of the mammalian glutamate transporter EAAT3. PLoS One (2014) 0.79
Exploring binding properties of agonists interacting with a δ-opioid receptor. PLoS One (2012) 0.78
Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles. Mol Simul (2009) 0.77
Modelling of Binding Free Energy of Targeted Nanocarriers to Cell Surface. Heat Mass Transf (2014) 0.75
Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations. Sci Rep (2015) 0.75
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
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
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
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
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
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
The transition state for peptide bond formation reveals the ribosome as a water trap. Proc Natl Acad Sci U S A (2010) 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
Mechanism of the translation termination reaction on the ribosome. Biochemistry (2009) 0.93
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
Structure-activity relationship for extracellular block of K+ channels by tetraalkylammonium ions. FEBS Lett (2003) 0.87
Continuum solvation models in the linear interaction energy method. J Phys Chem B (2006) 0.87
Force field independent metal parameters using a nonbonded dummy model. J Phys Chem B (2014) 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
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
Active site of epoxide hydrolases revisited: a noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate. Biochemistry (2007) 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
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
Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin. Proteins (2006) 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
Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum. Biochemistry (2006) 0.78
Does glutamine methylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors? Biochemistry (2009) 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
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
Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations. J Med Chem (2005) 0.77
Comparative analysis of putative agonist-binding modes in the human A1 adenosine receptor. Chembiochem (2004) 0.76
Mutagenesis and computational modeling of human G-protein-coupled receptor Y2 for neuropeptide Y and peptide YY. Biochemistry (2013) 0.76
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