Published in J Am Chem Soc on January 28, 2004
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
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
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
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J (2005) 4.26
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci U S A (2005) 4.15
Are current molecular dynamics force fields too helical? Biophys J (2008) 3.13
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A (2007) 2.24
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters. Nat Struct Mol Biol (2010) 2.20
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J Chem Theory Comput (2015) 2.20
Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J Chem Inf Model (2012) 2.17
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
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. J Chem Theory Comput (2012) 1.68
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins. J Chem Theory Comput (2013) 1.65
Embedded cholesterol in the nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (2008) 1.61
Two-stage folding of HP-35 from ab initio simulations. J Mol Biol (2007) 1.59
Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1. Nat Struct Mol Biol (2014) 1.58
Crystal structure of α5β1 integrin ectodomain: atomic details of the fibronectin receptor. J Cell Biol (2012) 1.52
Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain. Proc Natl Acad Sci U S A (2010) 1.48
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association. J Chem Theory Comput (2014) 1.47
Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water. Biophys J (2010) 1.47
Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A (2013) 1.41
Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structure-activity relationships of the nucleobase domain of 5'-O-[N-(salicyl)sulfamoyl]adenosine. J Med Chem (2008) 1.40
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain. Proc Natl Acad Sci U S A (2010) 1.33
Origin of the neighboring residue effect on peptide backbone conformation. Proc Natl Acad Sci U S A (2004) 1.32
Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties. Proteins (2005) 1.30
Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT. Biophys J (2012) 1.30
Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J Comput Chem (2006) 1.26
Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput (2013) 1.22
Functionally important conformations of the Met20 loop in dihydrofolate reductase are populated by rapid thermal fluctuations. J Am Chem Soc (2009) 1.22
Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry (2006) 1.21
Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J Mol Biol (2010) 1.19
Thermodynamic and structural basis of phosphorylation-induced disorder-to-order transition in the regulatory light chain of smooth muscle myosin. J Am Chem Soc (2008) 1.18
RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation. Biophys J (2010) 1.14
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase. Proc Natl Acad Sci U S A (2013) 1.14
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins (2011) 1.13
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
Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding. J Phys Chem B (2011) 1.11
Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. J Mol Biol (2010) 1.11
Rapid parameterization of small molecules using the Force Field Toolkit. J Comput Chem (2013) 1.10
Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci (2011) 1.09
Entropic stabilization of proteins by TMAO. J Phys Chem B (2011) 1.09
Molecular dynamics studies of ion permeation in VDAC. Biophys J (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
Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature (2015) 1.08
Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues. J Phys Chem B (2010) 1.07
Structure-guided forcefield optimization. Proteins (2011) 1.06
Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol (2007) 1.04
Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations. Biophys J (2007) 1.04
Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB. Elife (2014) 1.04
Conformational sampling of peptides in cellular environments. Biophys J (2007) 1.04
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM. J Biol Chem (2009) 1.03
Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods. J Biol Chem (2011) 1.03
General anesthetics predicted to block the GLIC pore with micromolar affinity. PLoS Comput Biol (2012) 1.02
Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations. J Phys Chem B (2012) 1.01
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochim Biophys Acta (2014) 1.01
Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. J Phys Chem B (2009) 1.01
Atomistic insights into rhodopsin activation from a dynamic model. J Am Chem Soc (2008) 1.00
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. J Chem Theory Comput (2012) 1.00
Unbiased simulations reveal the inward-facing conformation of the human serotonin transporter and Na(+) ion release. PLoS Comput Biol (2011) 1.00
The gating charge pathway of an epilepsy-associated potassium channel accommodates chemical ligands. Cell Res (2013) 1.00
PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins (2010) 0.99
High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase. Nat Commun (2014) 0.99
Computational studies of protegrin antimicrobial peptides: a review. Peptides (2010) 0.97
Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign. Biophys J (2012) 0.97
Product binding varies dramatically between processive and nonprocessive cellulase enzymes. J Biol Chem (2012) 0.96
Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem (2012) 0.96
Misplaced helix slows down ultrafast pressure-jump protein folding. Proc Natl Acad Sci U S A (2013) 0.95
Structural investigation of the transmembrane domain of KCNE1 in proteoliposomes. Biochemistry (2014) 0.95
Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J Biol Chem (2012) 0.95
Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J (2013) 0.95
How thioredoxin dissociates its mixed disulfide. PLoS Comput Biol (2009) 0.94
Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Phys Chem Chem Phys (2014) 0.94
Structural basis for the autoprocessing of zinc metalloproteases in the thermolysin family. Proc Natl Acad Sci U S A (2010) 0.94
Atomic-level characterization of the activation mechanism of SERCA by calcium. PLoS One (2011) 0.94
Pore dilatation increases the bicarbonate permeability of CFTR, ANO1 and glycine receptor anion channels. J Physiol (2016) 0.93
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study. Sci Rep (2015) 0.93
Comparative modeling of the human monoamine transporters: similarities in substrate binding. ACS Chem Neurosci (2012) 0.92
Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases. J Am Chem Soc (2013) 0.91
PRIMO: A Transferable Coarse-grained Force Field for Proteins. J Chem Theory Comput (2013) 0.91
Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. PLoS One (2011) 0.91
Biomolecular simulation and modelling: status, progress and prospects. J R Soc Interface (2008) 0.91
Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. J Chem Theory Comput (2013) 0.90
Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations. J Phys Chem B (2011) 0.90
Similarity measures for protein ensembles. PLoS One (2009) 0.90
Dynamics of cholesterol exchange in the oxysterol binding protein family. J Mol Biol (2008) 0.90
Binding and release of cholesterol in the Osh4 protein of yeast. Proteins (2009) 0.90
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Q Rev Biophys (2015) 0.89
A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering. Biophys J (2009) 0.89
Importance of the peptide backbone description in modeling the selectivity filter in potassium channels. Biophys J (2009) 0.89
Evidence that proline focuses movement of the floppy loop of arylalkylamine N-acetyltransferase (EC 2.3.1.87). J Biol Chem (2008) 0.89
Strandwise translocation of a DNA glycosylase on undamaged DNA. Proc Natl Acad Sci U S A (2012) 0.89
Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophys J (2010) 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
Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters. J Biol Chem (2015) 0.87
Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing. PLoS One (2011) 0.87
Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophys J (2015) 0.87
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97
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
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model (2004) 5.50
Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol (2004) 4.46
Generalized born model with a simple smoothing function. J Comput Chem (2003) 4.36
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem (2004) 3.83
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem (2003) 3.81
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A (2003) 3.64
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem (2003) 3.27
Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature (2005) 3.10
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91
The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci (2002) 2.81
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem (2004) 2.80
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
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol (2004) 2.78
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Constant-pH molecular dynamics using continuous titration coordinates. Proteins (2004) 2.52
Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci U S A (2003) 2.50
VIPERdb: a relational database for structural virology. Nucleic Acids Res (2006) 2.46
Constant pH molecular dynamics with proton tautomerism. Biophys J (2005) 2.44
Assessing scoring functions for protein-ligand interactions. J Med Chem (2004) 2.41
VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res (2008) 2.38
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct (2006) 2.24
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol (2002) 2.24
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A (2007) 2.24
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov (2009) 2.23
Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol (2008) 2.20
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol (2004) 2.19
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc Natl Acad Sci U S A (2003) 2.05
Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science (2011) 2.01
Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys (2004) 2.00
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol (2002) 1.98
Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry (2006) 1.88
A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys (2004) 1.86
Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins (2007) 1.83
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
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol (2005) 1.81
Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. J Mol Biol (2003) 1.76
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc Chem Res (2002) 1.69
Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A (2002) 1.68
Highly accurate biomolecular electrostatics in continuum dielectric environments. J Comput Chem (2008) 1.66
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci U S A (2005) 1.66
Albumin binding to FcRn: distinct from the FcRn-IgG interaction. Biochemistry (2006) 1.57
Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Lett (2007) 1.56
A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. J Chem Phys (2005) 1.56
A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol. Proc Natl Acad Sci U S A (2010) 1.55
Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci (2009) 1.52
Identifying native-like protein structures using physics-based potentials. J Comput Chem (2002) 1.51
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem (2005) 1.48
Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol Cell (2005) 1.43
Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci U S A (2007) 1.42
The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins (2004) 1.37
The effects of ionic strength on protein stability: the cold shock protein family. J Mol Biol (2002) 1.34
Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR (2004) 1.32
Evolution and physics in comparative protein structure modeling. Acc Chem Res (2002) 1.29
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 1.27
Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. J Chem Phys (2005) 1.27
Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U S A (2007) 1.26
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A (2006) 1.26
Lambda-dynamics free energy simulation methods. J Comput Chem (2009) 1.25
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys (2007) 1.25
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem (2011) 1.22
Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proc Natl Acad Sci U S A (2003) 1.21
Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry (2006) 1.21
De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. J Mol Biol (2004) 1.21
Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci U S A (2004) 1.21
A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model. J Chem Phys (2005) 1.21
Invariant polymorphism in virus capsid assembly. J Am Chem Soc (2009) 1.20
Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins (2013) 1.20
Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem (2005) 1.20
The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J Mol Biol (2005) 1.19
An electrostatic basis for the stability of thermophilic proteins. Proteins (2004) 1.19
Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci U S A (2006) 1.17
Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J Chem Theory Comput (2012) 1.17
The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. J Mol Biol (2005) 1.17
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. J Comput Chem (2006) 1.16
Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J Phys Chem B (2006) 1.16
A general method to quantify quasi-equivalence in icosahedral viruses. J Mol Biol (2002) 1.16
Evaluating CASP4 predictions with physical energy functions. Proteins (2002) 1.14
Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc (2004) 1.14
Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. J Am Chem Soc (2007) 1.14
Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol (2006) 1.14
An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins. Proc Natl Acad Sci U S A (2008) 1.13
Reduced native state stability in crowded cellular environment due to protein-protein interactions. J Am Chem Soc (2013) 1.13
Conformational substates modulate hydride transfer in dihydrofolate reductase. J Am Chem Soc (2005) 1.13
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR (2005) 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
How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc (2003) 1.11
Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem (2002) 1.11
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases. Biochem Cell Biol (2005) 1.11
Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". J Am Chem Soc (2005) 1.11
Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol (2008) 1.10
Aberrant activity of the DNA repair enzyme AlkB. J Inorg Biochem (2004) 1.10