Published in J Comput Chem on October 01, 2004
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem (2010) 8.79
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B (2010) 8.70
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
Molecular dynamics and protein function. Proc Natl Acad Sci U S A (2005) 4.70
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B (2008) 4.68
GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem (2008) 4.51
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci U S A (2005) 4.15
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B (2009) 3.17
Are current molecular dynamics force fields too helical? Biophys J (2008) 3.13
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J (2005) 2.84
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Conformation dependence of backbone geometry in proteins. Structure (2009) 2.33
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters. Nat Struct Mol Biol (2010) 2.20
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J Chem Inf Model (2012) 2.17
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput (2011) 2.12
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J (2005) 2.09
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. J Chem Theory Comput (2012) 2.07
Deformation and failure of protein materials in physiologically extreme conditions and disease. Nat Mater (2009) 2.00
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
Automated conformational energy fitting for force-field development. J Mol Model (2008) 1.84
Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state. Proc Natl Acad Sci U S A (2007) 1.82
Substrate binding and formation of an occluded state in the leucine transporter. Biophys J (2007) 1.77
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
The Design of a Next Generation Force Field: The X-POL Potential. J Chem Theory Comput (2007) 1.68
Discovery through the computational microscope. Structure (2009) 1.67
Force field bias in protein folding simulations. Biophys J (2009) 1.67
Slowing down DNA translocation through a nanopore in lithium chloride. Nano Lett (2012) 1.63
Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields. Biophys J (2006) 1.61
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
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
Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition. J Am Chem Soc (2011) 1.45
Structural basis for microtubule binding and release by dynein. Science (2012) 1.45
Polarization effects in molecular mechanical force fields. J Phys Condens Matter (2009) 1.41
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res (2010) 1.40
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol (2009) 1.27
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
A novel mechanism by which thiazolidinediones facilitate the proteasomal degradation of cyclin D1 in cancer cells. J Biol Chem (2008) 1.22
A new generation of statistical potentials for proteins. Biophys J (2006) 1.22
MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem (2011) 1.22
Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations. J Comput Chem (2012) 1.20
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J Comput Chem (2007) 1.18
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins (2011) 1.16
The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response. Nucleic Acids Res (2006) 1.16
A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations. PLoS Comput Biol (2012) 1.15
Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions. Biointerphases (2008) 1.14
A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values. Protein Sci (2008) 1.13
Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys (2011) 1.12
CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. J Phys Chem B (2010) 1.12
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys J (2012) 1.12
Interfacial tryptophan residues: a role for the cation-pi effect? Biophys J (2005) 1.11
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. Nucleic Acids Res (2007) 1.10
Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci (2011) 1.09
Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. PLoS Comput Biol (2012) 1.08
Emerging methods for ensemble-based virtual screening. Curr Top Med Chem (2010) 1.08
Structural biology by NMR: structure, dynamics, and interactions. PLoS Comput Biol (2008) 1.07
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B (2010) 1.07
Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects. Drug Discov Today (2010) 1.07
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B (2010) 1.07
Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation. Elife (2016) 1.06
Many-body polarization effects and the membrane dipole potential. J Am Chem Soc (2009) 1.06
Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes. Biophys J (2009) 1.06
Early events in helix unfolding under external forces: a milestoning analysis. J Phys Chem B (2012) 1.05
AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA. J Chem Theory Comput (2013) 1.05
Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations. Biophys J (2007) 1.04
Conformational sampling of peptides in cellular environments. Biophys J (2007) 1.04
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers. J Mol Model (2009) 1.04
Mechanical properties of a complete microtubule revealed through molecular dynamics simulation. Biophys J (2010) 1.03
Modeling and simulation of ion channels. Chem Rev (2012) 1.02
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state. Mol Biosyst (2010) 1.01
Design of protein-ligand binding based on the molecular-mechanics energy model. J Mol Biol (2008) 1.01
A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B (2013) 1.01
Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra. Biophys J (2006) 1.00
Classical electrostatics for biomolecular simulations. Chem Rev (2013) 1.00
Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study. Nucleic Acids Res (2008) 0.99
The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One (2011) 0.98
Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics. Biointerphases (2008) 0.97
Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model. J Phys Chem Lett (2014) 0.97
Intrinsically disordered proteins in a physics-based world. Int J Mol Sci (2010) 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
Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes. Biophys J (2009) 0.96
Viral genome structures are optimal for capsid assembly. Elife (2013) 0.96
The lipopolysaccharide from Capnocytophaga canimorsus reveals an unexpected role of the core-oligosaccharide in MD-2 binding. PLoS Pathog (2012) 0.96
Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin. J Biol Chem (2010) 0.96
Misplaced helix slows down ultrafast pressure-jump protein folding. Proc Natl Acad Sci U S A (2013) 0.95
Interaction of the complexin accessory helix with the C-terminus of the SNARE complex: molecular-dynamics model of the fusion clamp. Biophys J (2013) 0.95
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Thiazolidinediones mimic glucose starvation in facilitating Sp1 degradation through the up-regulation of beta-transducin repeat-containing protein. Mol Pharmacol (2009) 0.95
Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. J Phys Chem Lett (2012) 0.94
Incorporating Phase-Dependent Polarizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid-Vapor Interface. J Chem Theory Comput (2009) 0.94