Published in J Chem Phys on July 22, 2005
Towards a force field based on density fitting. J Chem Phys (2006) 1.70
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
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
Contracted auxiliary Gaussian basis integral and derivative evaluation. J Chem Phys (2008) 1.24
Gaussian Multipole Model (GMM). J Chem Theory Comput (2010) 1.02
Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations. J Chem Theory Comput (2014) 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
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities. J Comput Chem (2008) 0.90
Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions. J Chem Theory Comput (2014) 0.87
Atomic forces for geometry-dependent point multipole and gaussian multipole models. J Comput Chem (2010) 0.83
Limiting assumptions in molecular modeling: electrostatics. J Comput Aided Mol Des (2013) 0.81
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem (2016) 0.80
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B Condens Matter (1988) 93.32
Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution. J Phys Chem A (2003) 1.77
A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution. J Comput Chem (2005) 1.68
Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: a new efficient method to study intermolecular interaction energies. J Chem Phys (2005) 1.30
Calculation of electrostatic and polarization energies from electron densities. J Chem Phys (2004) 0.96
Second-order Møller-Plesset theory with linear R12 terms (MP2-R12) revisited: auxiliary basis set method and massively parallel implementation. J Chem Phys (2004) 0.96
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
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
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
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
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
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
Predicted solution structure of zymogen human coagulation FVII. J Comput Chem (2002) 0.86
[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
Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B (2014) 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
S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. J Phys Chem A (2014) 0.82
Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Phys Chem Chem Phys (2011) 0.82
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 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
Dioxygen activation by mononuclear copper enzymes: insights from a tripodal ligand mimicking their Cu(M) coordination sphere. Inorg Chem (2009) 0.77
Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion. Chemistry (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
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
Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? J Comput Chem (2013) 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
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
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
Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations. J Chem Phys (2004) 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
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
Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination. J Comput Chem (2015) 0.75
Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-β-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry. J Phys Chem B (2017) 0.75
Understanding lead chemistry from topological insights: the transition between holo- and hemidirected structures within the [Pb(CO)n]2+ model series. Chemistry (2008) 0.75
Capturing Many-body Interactions with Classical Dipole Induction Models. J Chem Theory Comput (2017) 0.75
Editorial: special issue on quantum mechanical modeling of biological systems. Interdiscip Sci (2010) 0.75
Characterizing Molecular Interactions in Chemical Systems. IEEE Trans Vis Comput Graph (2014) 0.75
Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics. J Mol Model (2014) 0.75
Spin-driven activation of dioxygen in various metalloenzymes and their inspired models. J Comput Chem (2010) 0.75
Three-dimensional solution structure of Tropidechis carinatus venom extract trocarin: a structural homologue of Xa and prothrombin activator. J Mol Model (2002) 0.75