Published in Biophys J on July 01, 2007
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
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
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
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
The effect of electrostatic interactions on conformational equilibria of multiply substituted tetrahydropyran oxocarbenium ions. J Org Chem (2009) 1.07
Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. J Comput Chem (2013) 0.92
Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran. J Am Chem Soc (2008) 0.86
Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys (2006) 6.51
Comparative performance of MM3(92) and two TINKER MM3 versions for the modeling of carbohydrates. J Comput Chem (2005) 1.16
Intrinsic conformational preferences of substituted cyclohexanes and tetrahydropyrans evaluated at the CCSD(T) complete basis set limit: implications for the anomeric effect. J Phys Chem A (2005) 1.16
The correlation consistent composite approach (ccCA): an alternative to the Gaussian-n methods. J Chem Phys (2006) 1.10
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B (2010) 8.70
An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J Phys Chem B (2005) 3.32
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys J (2005) 2.84
An evaluation of harmonic vibrational frequency scale factors. J Phys Chem A (2007) 2.82
Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties. J Am Chem Soc (2002) 2.76
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
Polarizable empirical force field for alkanes based on the classical Drude oscillator model. J Phys Chem B (2005) 2.56
Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs. Cell (2011) 2.55
Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophys J (2006) 2.30
Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. J Mol Biol (2002) 1.95
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A (2006) 1.90
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J Comput Chem (2007) 1.86
Automated conformational energy fitting for force-field development. J Mol Model (2008) 1.84
CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem (2013) 1.82
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A (2002) 1.78
The structure of aqueous guanidinium chloride solutions. J Am Chem Soc (2004) 1.66
Computational fragment-based binding site identification by ligand competitive saturation. PLoS Comput Biol (2009) 1.61
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (2005) 1.60
Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B (2008) 1.57
Isotropic periodic sum: a method for the calculation of long-range interactions. J Chem Phys (2005) 1.53
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proc Natl Acad Sci U S A (2008) 1.52
Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method. J Phys Chem B (2007) 1.49
A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose. Biophys J (2005) 1.42
Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction. J Med Chem (2004) 1.41
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J (2002) 1.40
Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics. Biophys J (2008) 1.39
CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model (2008) 1.38
Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inf Comput Sci (2003) 1.37
A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics. J Phys Chem B (2009) 1.37
Normal-modes-based prediction of protein conformational changes guided by distance constraints. Biophys J (2005) 1.37
2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists. J Am Chem Soc (2003) 1.36
Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res (2008) 1.36
A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J Struct Biol (2003) 1.36
Single molecule diffusion of membrane-bound proteins: window into lipid contacts and bilayer dynamics. Biophys J (2010) 1.35
Computational approaches for investigating base flipping in oligonucleotides. Chem Rev (2006) 1.35
Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study. Biophys J (2008) 1.34
Is arginine charged in a membrane? Biophys J (2007) 1.33
Self-guided Langevin dynamics study of regulatory interactions in NtrC. Proteins (2009) 1.32
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. J Comput Chem (2002) 1.32
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J (2007) 1.31
Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. EMBO J (2002) 1.30
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy. Biophys J (2008) 1.30
Dynamical motions of lipids and a finite size effect in simulations of bilayers. J Chem Phys (2006) 1.30
A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep (2013) 1.28
Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol (2009) 1.27
Protein conformational transitions explored by mixed elastic network models. Proteins (2007) 1.26
Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. J Comput Chem (2009) 1.24
Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation. J Am Chem Soc (2002) 1.23
Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity. J Med Chem (2007) 1.22
Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions. Biophys J (2002) 1.21
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys J (2005) 1.20
Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations. J Comput Chem (2012) 1.20
Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol (2008) 1.19
Multiscale methods for macromolecular simulations. Curr Opin Struct Biol (2008) 1.19
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J Comput Chem (2007) 1.18
All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem (2014) 1.16
Molecular dynamics simulations of the influenza hemagglutinin fusion peptide in micelles and bilayers: conformational analysis of peptide and lipids. J Mol Biol (2005) 1.16
A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo. PLoS One (2012) 1.15
Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. J Mol Biol (2007) 1.15
Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J (2012) 1.15
Computational identification of inhibitors of protein-protein interactions. Curr Top Med Chem (2007) 1.14
Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems. J Chem Phys (2008) 1.14
Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water. Biophys J (2004) 1.13
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
Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers. J Phys Chem B (2009) 1.12
Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. J Mol Biol (2010) 1.11
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10
Structure and dynamics of helix-0 of the N-BAR domain in lipid micelles and bilayers. Biophys J (2008) 1.10
Annealing function of GroEL: structural and bioinformatic analysis. Biophys Chem (2003) 1.10
Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J Chem Inf Model (2013) 1.09
Divalent metal ion complexes of S100B in the absence and presence of pentamidine. J Mol Biol (2008) 1.09
Molecular dynamics studies of ion permeation in VDAC. Biophys J (2011) 1.09
Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages. Mol Biol Cell (2011) 1.09
Toward canonical ensemble distribution from self-guided Langevin dynamics simulation. J Chem Phys (2011) 1.08
Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. J Med Chem (2004) 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
Depth of α-synuclein in a bilayer determined by fluorescence, neutron reflectometry, and computation. Biophys J (2012) 1.06
Molecular dynamics simulations of PIP2 and PIP3 in lipid bilayers: determination of ring orientation, and the effects of surface roughness on a Poisson-Boltzmann description. Biophys J (2009) 1.05
Discriminating the helical forms of peptides by NMR and molecular dynamics simulation. J Am Chem Soc (2004) 1.05
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Proc Natl Acad Sci U S A (2012) 1.05
Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics. Adv Chem Phys (2012) 1.05
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res (2003) 1.05
The molecular structure of the liquid-ordered phase of lipid bilayers. J Am Chem Soc (2014) 1.05
Atomistic view of base flipping in DNA. Philos Trans A Math Phys Eng Sci (2004) 1.05
pH replica-exchange method based on discrete protonation states. Proteins (2011) 1.04
Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. J Phys Chem B (2005) 1.04
The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer (2013) 1.04
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res (2004) 1.03