Published in J Comput Chem on September 01, 2009
CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem (2013) 1.82
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. J Chem Theory Comput (2011) 1.55
Polarization effects in molecular mechanical force fields. J Phys Condens Matter (2009) 1.41
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.39
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.24
Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput (2013) 1.22
All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem (2014) 1.16
Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci (2011) 1.09
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B (2010) 1.07
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers. J Mol Model (2009) 1.04
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochim Biophys Acta (2014) 1.01
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field. J Phys Chem B (2014) 0.94
Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator. J Phys Chem B (2014) 0.93
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chem Rev (2016) 0.91
Polarizable empirical force field for acyclic polyalcohols based on the classical drude oscillator. Biopolymers (2013) 0.88
Current status of protein force fields for molecular dynamics simulations. Methods Mol Biol (2015) 0.81
Molecular mechanics. Curr Pharm Des (2014) 0.81
Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J Chem Phys (2013) 0.81
Matching of additive and polarizable force fields for multiscale condensed phase simulations. J Chem Theory Comput (2013) 0.78
Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective. J Mol Model (2013) 0.78
Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model. J Comput Chem (2012) 0.77
CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides. J Phys Chem B (2015) 0.77
Metal Ion Modeling Using Classical Mechanics. Chem Rev (2017) 0.75
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J Comput Aided Mol Des (2017) 0.75
The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B (2002) 234.73
All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00
Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A Gen Phys (1988) 39.03
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem (2004) 8.13
Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem (2004) 3.65
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comput Chem (2002) 3.11
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem (2004) 2.80
Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem Rev (1999) 2.58
Polarizable empirical force field for alkanes based on the classical Drude oscillator model. J Phys Chem B (2005) 2.56
Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. J Chem Theory Comput (2005) 2.02
Noncovalent interactions: a challenge for experiment and theory. Chem Rev (2000) 1.96
Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput (2007) 1.86
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B (2007) 1.77
High-accuracy quantum mechanical studies of pi-pi interactions in benzene dimers. J Phys Chem A (2006) 1.67
Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. J Am Chem Soc (2002) 1.54
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J Chem Phys (2007) 1.33
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. J Comput Chem (2002) 1.32
Optimization of effective atom centered potentials for london dispersion forces in density functional theory. Phys Rev Lett (2004) 1.32
Interaction energy contributions of H-bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach. J Am Chem Soc (2006) 1.13
The polarizability of point-polarizable water models: density functional theory/molecular mechanics results. J Phys Chem B (2008) 1.11
Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes. J Phys Chem A (2007) 0.96
Pi-pi interaction in pyridine. J Phys Chem A (2005) 0.94
A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide. J Chem Phys (2004) 0.93
Van der Waals interactions in aromatic systems: structure and energetics of dimers and trimers of pyridine. Chemphyschem (2005) 0.90
Evaluation of the molecular polarizability using the IPPP-CLOPPA-INDO/S method. Application to molecules of biological interest. J Phys Chem A (2008) 0.87
Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT. J Phys Chem B (2007) 0.83
The crystal and molecular structure of purine. Acta Crystallogr (1965) 0.82
A new insight into the vibrational analysis of pyridine. Spectrochim Acta A Mol Biomol Spectrosc (2003) 0.81
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010) 3.05
CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem (2004) 2.79
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput (2012) 1.93
Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput (2007) 1.86
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem (2011) 1.81
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B (2007) 1.77
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol. J Chem Theory Comput (2009) 1.68
Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol. Biochemistry (2004) 1.62
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc (2009) 1.54
CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. J Chem Theory Comput (2011) 1.51
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. J Phys Chem Lett (2011) 1.41
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field. J Phys Chem B (2005) 1.39
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.39
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy. Biophys J (2008) 1.30
NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J Am Chem Soc (2006) 1.29
Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput (2007) 1.28
Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. J Chem Inf Model (2011) 1.26
Identification of novel extracellular signal-regulated kinase docking domain inhibitors. J Med Chem (2005) 1.25
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.24
CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field. J Comput Chem (2005) 1.13
Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding. J Phys Chem A (2006) 1.13
A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. J Chem Theory Comput (2007) 1.13
Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem (2008) 1.11
Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci (2011) 1.09
Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter. J Med Chem (2010) 1.07
Many-body polarization effects and the membrane dipole potential. J Am Chem Soc (2009) 1.06
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers. J Mol Model (2009) 1.04
Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation. Proteins (2004) 1.03
Computational ligand-based rational design: Role of conformational sampling and force fields in model development. Medchemcomm (2011) 1.01
Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates. Mol Pharm (2010) 1.01
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. J Chem Theory Comput (2011) 1.00
Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. PLoS Pathog (2013) 0.97
Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Curr Comput Aided Drug Des (2011) 0.97
Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. J Am Chem Soc (2009) 0.94
Development of an empirical force field for silica. Application to the quartz-water interface. J Phys Chem B (2006) 0.94
Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor. Nucleic Acids Res (2012) 0.93
Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J Struct Biol (2006) 0.92
Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin. ACS Med Chem Lett (2012) 0.89
Inhibition requirements of the human apical sodium-dependent bile acid transporter (hASBT) using aminopiperidine conjugates of glutamyl-bile acids. Pharm Res (2009) 0.89
Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach. PLoS Comput Biol (2013) 0.88
Design of Inhibitors for S100B. Curr Top Med Chem (2005) 0.88
Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. J Chem Theory Comput (2012) 0.88
Mitogen activated protein (MAP) kinases: development of ATP and non-ATP dependent inhibitors. Med Chem (2006) 0.88
Polarizable empirical force field for acyclic polyalcohols based on the classical drude oscillator. Biopolymers (2013) 0.88
Ammonium transporters achieve charge transfer by fragmenting their substrate. J Am Chem Soc (2012) 0.88
Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes. Mol Pharm (2008) 0.87
Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study. J Phys Chem B (2008) 0.86
Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies. J Mol Biol (2011) 0.86
Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement. J Med Chem (2010) 0.85
Targeting protein tyrosine phosphatase SHP2 for the treatment of PTPN11-associated malignancies. Mol Cancer Ther (2013) 0.85
Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade. J Med Chem (2011) 0.84
Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. J Phys Chem B (2010) 0.83
Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin. ACS Med Chem Lett (2012) 0.83
Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B. ACS Med Chem Lett (2012) 0.83
Using Caenorhabditis elegans as a model organism for evaluating extracellular signal-regulated kinase docking domain inhibitors. J Cell Commun Signal (2008) 0.81
Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations. J Am Chem Soc (2011) 0.80
Hydrophobic residues in small ankyrin 1 participate in binding to obscurin. Mol Membr Biol (2012) 0.80
Putative irreversible inhibitors of the human sodium-dependent bile acid transporter (hASBT; SLC10A2) support the role of transmembrane domain 7 in substrate binding/translocation. Pharm Res (2012) 0.80
Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach. J Phys Chem Lett (2011) 0.79
Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness. J Chem Inf Model (2010) 0.79
Identification of novel nonsteroidal compounds as substrates or inhibitors of hASBT. J Pharm Sci (2011) 0.78
Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface. J Phys Chem B (2010) 0.78
Inhibition of protein-protein interactions with low molecular weight compounds. Curr Trends Med Chem (2008) 0.77
Characterizing structural transitions using localized free energy landscape analysis. PLoS One (2009) 0.77
Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation. J Phys Chem B (2007) 0.76
Different hydration patterns in the pores of AmtB and RhCG could determine their transport mechanisms. Biochemistry (2013) 0.76
Synthesis and Characterization of a Novel Diels - Alder Adduct of Codeine. Helv Chim Acta (2010) 0.75
Correction to intrinsic energy landscapes of amino acid side-chains. J Chem Inf Model (2012) 0.75
Salt-dependent Interactions Between the C-terminal Domain of Osmoregulatory Transporter ProP of and the Lipid Membrane. J Phys Chem B (2020) 0.75