Published in J Phys Chem A on June 19, 2014
Multipolar Ewald methods, 1: theory, accuracy, and performance. J Chem Theory Comput (2015) 0.85
Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev (2016) 0.84
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J Comput Chem (2016) 0.81
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem (2016) 0.80
Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids. J Phys Chem B (2015) 0.79
Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations. J Chem Phys (2015) 0.75
Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations. J Chem Phys (2004) 2.32
NCIPLOT: a program for plotting non-covalent interaction regions. J Chem Theory Comput (2011) 2.17
Differential transactivation by the p53 transcription factor is highly dependent on p53 level and promoter target sequence. Mol Cell Biol (2002) 1.83
Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A (2008) 1.75
NMDA receptor activation by HIV-Tat protein is clade dependent. J Neurosci (2008) 1.74
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B (2006) 1.73
Towards a force field based on density fitting. J Chem Phys (2006) 1.70
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. J Chem Phys (2006) 1.69
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput (2007) 1.58
Intermolecular electrostatic energies using density fitting. J Chem Phys (2005) 1.42
Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. J Chem Phys (2006) 1.34
Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields. J Chem Phys (2004) 1.33
Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility. J Chem Theory Comput (2009) 1.16
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem (2005) 1.10
Polarizable molecular dynamics simulation of Zn(II) in water using the AMOEBA force field. J Chem Theory Comput (2010) 1.07
Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA. J Biol Chem (2002) 1.05
Glucosaminylglycan biosynthesis: what we can learn from the X-ray crystal structures of glycosyltransferases GlcAT1 and EXTL2. Biochem Biophys Res Commun (2003) 1.05
Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. J Am Chem Soc (2007) 1.03
Conformations and free energy landscapes of polyproline peptides. Proc Natl Acad Sci U S A (2009) 1.03
Design, synthesis, and biological evaluation of novel naphthoquinone derivatives with CDC25 phosphatase inhibitory activity. Bioorg Med Chem (2005) 1.03
Gaussian Multipole Model (GMM). J Chem Theory Comput (2010) 1.02
Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. J Phys Chem B (2006) 1.01
Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput (2012) 1.01
Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments. J Comput Chem (2008) 0.99
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. J Comput Chem (2003) 0.99
Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. J Mol Biol (2008) 0.98
Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. J Comput Chem (2005) 0.97
Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc (2009) 0.95
The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections. J Chem Phys (2006) 0.93
Surface solvation for an ion in a water cluster. J Chem Phys (2005) 0.92
Numerical fitting of molecular properties to Hermite Gaussians. J Phys Chem A (2007) 0.91
Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. J Phys Chem B (2006) 0.90
Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. J Phys Chem B (2013) 0.88
Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (M(p+) = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+). J Comput Chem (2006) 0.88
Coupling quantum interpretative techniques: another look at chemical mechanisms in organic reactions. J Chem Theory Comput (2012) 0.87
Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe. J Am Chem Soc (2012) 0.87
Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem (2002) 0.86
Polarizable water molecules in ligand-macromolecule recognition. Impact on the relative affinities of competing pyrrolopyrimidine inhibitors for FAK kinase. J Am Chem Soc (2010) 0.86
Key role of the polarization anisotropy of water in modeling classical polarizable force fields. J Phys Chem A (2007) 0.86
Predicted solution structure of zymogen human coagulation FVII. J Comput Chem (2002) 0.86
Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids. J Phys Chem B (2014) 0.84
Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B (2014) 0.83
[Pb(H2O)]2+ and [Pb(OH)]+: four-component density functional theory calculations, correlated scalar relativistic constrained-space orbital variation energy decompositions, and topological analysis. J Chem Phys (2006) 0.83
Mapping the dimer interface in the C-terminal domains of the yeast MLH1-PMS1 heterodimer. Biochemistry (2006) 0.83
Polarizable water networks in ligand-metalloprotein recognition. Impact on the relative complexation energies of Zn-dependent phosphomannose isomerase with D-mannose 6-phosphate surrogates. J Phys Chem B (2011) 0.82
Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem (2007) 0.82
Novel 1,4-benzodiazepine derivatives with antiproliferative properties on tumor cell lines. Bioorg Med Chem Lett (2007) 0.82
Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Phys Chem Chem Phys (2011) 0.82
Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition. PLoS One (2012) 0.81
Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways. J Phys Chem B (2012) 0.81
Synthesis and evaluation of non-hydrolyzable D-mannose 6-phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-D-mannose as a new strong inhibitor of phosphomannose isomerases. Bioorg Med Chem (2009) 0.81
The kinase activity of the Helicobacter pylori Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase is sensitive to distal mutations in its putative ammonia tunnel. Biochemistry (2011) 0.79
The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins (2011) 0.79
Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models. J Mol Struct (2006) 0.78
Analysis of the interactions taking place in the recognition site of a bimetallic Mg(II)-Zn(II) enzyme, isopentenyl diphosphate isomerase. a parallel quantum-chemical and polarizable molecular mechanics study. J Phys Chem B (2010) 0.78
Efficient optimization of van der Waals parameters from bulk properties. J Comput Chem (2013) 0.78
Potent inhibitors of CDK5 derived from roscovitine: synthesis, biological evaluation and molecular modelling. Bioorg Med Chem Lett (2012) 0.77
Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. Biochemistry (2009) 0.77
Many-body exchange-repulsion in polarizable molecular mechanics. I. Orbital-based approximations and applications to hydrated metal cation complexes. J Comput Chem (2011) 0.77
A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field. J Comput Chem (2014) 0.77
Dioxygen activation by mononuclear copper enzymes: insights from a tripodal ligand mimicking their Cu(M) coordination sphere. Inorg Chem (2009) 0.77
Novel alkoxide cluster topologies featuring rare seesaw geometry at transition metal centers. Chemistry (2013) 0.77
Novel naphthoquinone and quinolinedione inhibitors of CDC25 phosphatase activity with antiproliferative properties. Bioorg Med Chem (2008) 0.77
Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion. Chemistry (2011) 0.77
Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB). J Phys Chem B (2015) 0.76
Substituent-modulated affinities of halobenzene derivatives to the HIV-1 integrase recognition site. Analyses of the interaction energies by parallel quantum chemical and polarizable molecular mechanics. J Phys Chem A (2014) 0.76
Synthesis of aryl phosphates based on pyrimidine and triazine scaffolds. Eur J Med Chem (2009) 0.76
Entasis through hook-and-loop fastening in a glycoligand with cumulative weak forces stabilizing Cu(I). J Am Chem Soc (2015) 0.76
Polarizable molecular dynamics in a polarizable continuum solvent. J Chem Theory Comput (2015) 0.76
Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I. Biochemistry (2012) 0.76
Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? J Comput Chem (2013) 0.76
Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations. J Comput Chem (2014) 0.75
Could the "Janus-like" properties of the halobenzene CX bond (X=Cl, Br) be leveraged to enhance molecular recognition? J Comput Chem (2014) 0.75
Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: bimetallic binding site and structured waters. J Comput Chem (2014) 0.75