Published in J Phys Chem B on April 30, 1998
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
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
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
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
Structure and function of an irreversible agonist-β(2) adrenoceptor complex. Nature (2011) 5.35
GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem (2008) 4.51
Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys J (2005) 4.45
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins (2009) 4.27
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc Natl Acad Sci U S A (2005) 4.15
The dynamic process of β(2)-adrenergic receptor activation. Cell (2013) 4.09
ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nat Genet (2013) 4.03
Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature (2012) 3.83
Tools for comparative protein structure modeling and analysis. Nucleic Acids Res (2003) 3.68
Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc Natl Acad Sci U S A (2002) 3.60
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. Proc Natl Acad Sci U S A (2003) 3.34
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci U S A (2002) 3.23
Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci U S A (2005) 3.21
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods (2010) 3.07
Current status of the AMOEBA polarizable force field. J Phys Chem B (2010) 3.06
Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel. Proc Natl Acad Sci U S A (2005) 3.06
Nanoconfinement controls stiffness, strength and mechanical toughness of beta-sheet crystals in silk. Nat Mater (2010) 3.06
A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010) 3.05
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature (2011) 3.00
Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure (2008) 2.98
Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci U S A (2005) 2.92
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91
Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B (2009) 2.80
Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J Gen Physiol (2007) 2.79
Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci U S A (2009) 2.77
Theory and simulation of water permeation in aquaporin-1. Biophys J (2004) 2.63
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc Natl Acad Sci U S A (2005) 2.61
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
Activation mechanism of the β2-adrenergic receptor. Proc Natl Acad Sci U S A (2011) 2.53
Principles of conduction and hydrophobic gating in K+ channels. Proc Natl Acad Sci U S A (2010) 2.47
The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure (2007) 2.45
High-resolution crystal structure of human protease-activated receptor 1. Nature (2012) 2.44
Constant pH molecular dynamics with proton tautomerism. Biophys J (2005) 2.44
Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. Proc Natl Acad Sci U S A (2010) 2.43
Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J (2011) 2.43
Platelet glycoprotein Ibalpha forms catch bonds with human WT vWF but not with type 2B von Willebrand disease vWF. J Clin Invest (2008) 2.43
Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods (2009) 2.39
Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 2.37
Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. Proc Natl Acad Sci U S A (1999) 2.36
Electrostatic tuning of permeation and selectivity in aquaporin water channels. Biophys J (2003) 2.31
Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys J (2004) 2.30
Systematic validation of protein force fields against experimental data. PLoS One (2012) 2.29
How proteins trigger excitation energy transfer in the FMO complex of green sulfur bacteria. Biophys J (2006) 2.28
Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms. J Mol Biol (2008) 2.27
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol (2008) 2.27
Mechanisms and free energies of enzymatic reactions. Chem Rev (2006) 2.25
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A (2009) 2.25
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Biophys J (2003) 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
Is the first hydration shell of lysozyme of higher density than bulk water? Proc Natl Acad Sci U S A (2002) 2.19
Prediction of structure and function of G protein-coupled receptors. Proc Natl Acad Sci U S A (2002) 2.19
Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc Natl Acad Sci U S A (2000) 2.18
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Structure and hydration of membranes embedded with voltage-sensing domains. Nature (2009) 2.15
Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide. EMBO J (2005) 2.12
Transient non-native hydrogen bonds promote activation of a signaling protein. Cell (2009) 2.12
The hidden energetics of ligand binding and activation in a glutamate receptor. Nat Struct Mol Biol (2011) 2.10
Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment. Biophys J (2007) 2.10
How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci U S A (2002) 2.06
Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol (2008) 2.05
A two-domain elevator mechanism for sodium/proton antiport. Nature (2013) 2.05
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci U S A (2008) 2.03
Flow-enhanced adhesion regulated by a selectin interdomain hinge. J Cell Biol (2006) 2.02
H bonding at the helix-bundle crossing controls gating in Kir potassium channels. Neuron (2007) 2.02
Design of therapeutic proteins with enhanced stability. Proc Natl Acad Sci U S A (2009) 2.01
Four-scale description of membrane sculpting by BAR domains. Biophys J (2008) 2.00
Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS. Biophys J (2004) 2.00
Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys (2007) 1.99
Amyloid beta-protein monomer structure: a computational and experimental study. Protein Sci (2006) 1.99
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics. Proc Natl Acad Sci U S A (2010) 1.97
Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. Proc Natl Acad Sci U S A (2005) 1.97
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proc Natl Acad Sci U S A (2009) 1.93
Forced detachment of the CD2-CD58 complex. Biophys J (2003) 1.92
Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophys J (2004) 1.91
Validation of the 53A6 GROMOS force field. Eur Biophys J (2005) 1.91
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure (2010) 1.91
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
Ab initio quantum chemistry: methodology and applications. Proc Natl Acad Sci U S A (2005) 1.88
On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J Gen Physiol (2004) 1.88
Water and proton conduction through carbon nanotubes as models for biological channels. Biophys J (2003) 1.87
Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophys J (2010) 1.87
Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput (2007) 1.86
The mitochondrial calcium uniporter is a multimer that can include a dominant-negative pore-forming subunit. EMBO J (2013) 1.86
Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proc Natl Acad Sci U S A (2003) 1.86
A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. Proc Natl Acad Sci U S A (2006) 1.84
Automated conformational energy fitting for force-field development. J Mol Model (2008) 1.84
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84
Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci (2005) 1.83
CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem (2013) 1.82
Ion conduction through MscS as determined by electrophysiology and simulation. Biophys J (2006) 1.80
Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin. Biophys J (2006) 1.80
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Crystallographic R factor refinement by molecular dynamics. Science (1987) 15.90
Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res (1989) 15.35
Effective energy function for proteins in solution. Proteins (1999) 9.44
A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res (1990) 8.52
Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins (2000) 8.17
Dynamics of folded proteins. Nature (1977) 7.82
Urban residential environments and senior citizens' longevity in megacity areas: the importance of walkable green spaces. J Epidemiol Community Health (2002) 7.79
How does a protein fold? Nature (1994) 7.55
Methylmercury poisoning in Iraq. Science (1973) 6.84
Evaluation of comparative protein modeling by MODELLER. Proteins (1995) 6.42
Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol (1993) 6.26
Functional arteries grown in vitro. Science (1999) 6.08
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry (1990) 5.92
Energetics of ion conduction through the K+ channel. Nature (2001) 5.69
Overview of the National Infant Mortality Surveillance (NIMS) project--design, methods, results. Public Health Rep (1987) 5.66
DIAN: a novel algorithm for genome ontological classification. Genome Res (2001) 5.55
Silberblick/Wnt11 mediates convergent extension movements during zebrafish gastrulation. Nature (2000) 5.52
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1983) 5.27
Epilepsy and exacerbation of brain injury in mice lacking the glutamate transporter GLT-1. Science (1997) 5.13
Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med (1999) 5.12
Major susceptibility locus for prostate cancer on chromosome 1 suggested by a genome-wide search. Science (1996) 5.06
A general solution to the time interval omission problem applied to single channel analysis. Biophys J (1985) 5.04
PTEN modulates cell cycle progression and cell survival by regulating phosphatidylinositol 3,4,5,-trisphosphate and Akt/protein kinase B signaling pathway. Proc Natl Acad Sci U S A (1999) 4.90
Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science (1987) 4.89
Parkin functions as an E2-dependent ubiquitin- protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1. Proc Natl Acad Sci U S A (2000) 4.83
Autotrophic picoplankton in the tropical ocean. Science (1983) 4.80
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol (1997) 4.79
The internal dynamics of globular proteins. CRC Crit Rev Biochem (1981) 4.59
Dynamics of proteins: elements and function. Annu Rev Biochem (1983) 4.56
Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins (1991) 4.53
Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana. Proc Natl Acad Sci U S A (1996) 4.48
Parkin ubiquitinates the alpha-synuclein-interacting protein, synphilin-1: implications for Lewy-body formation in Parkinson disease. Nat Med (2001) 4.22
Protein-folding dynamics. Nature (1976) 4.11
Aortic homograft valve replacement. A long-term follow-up of an initial series of 101 patients. Circulation (1969) 4.10
Xwnt11 is a target of Xenopus Brachyury: regulation of gastrulation movements via Dishevelled, but not through the canonical Wnt pathway. Development (2000) 4.06
"New view" of protein folding reconciled with the old through multiple unfolding simulations. Science (1997) 3.93
SOX10 mutations in patients with Waardenburg-Hirschsprung disease. Nat Genet (1998) 3.82
Smad4 and FAST-1 in the assembly of activin-responsive factor. Nature (1997) 3.66
In utero antiepileptic drug exposure: fetal death and malformations. Neurology (2006) 3.64
Risk factors for myocardial infarction and death in newly detected NIDDM: the Diabetes Intervention Study, 11-year follow-up. Diabetologia (1996) 3.62
X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution. J Mol Biol (1986) 3.49
APC mutations in sporadic colorectal tumors: A mutational "hotspot" and interdependence of the "two hits". Proc Natl Acad Sci U S A (2000) 3.41
Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophys J (1991) 3.38
Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. J Mol Biol (1989) 3.37
Picosecond dynamics of tyrosine side chains in proteins. Biochemistry (1979) 3.35
Dynamics of ligand binding to heme proteins. J Mol Biol (1979) 3.35
SIP1, a novel zinc finger/homeodomain repressor, interacts with Smad proteins and binds to 5'-CACCT sequences in candidate target genes. J Biol Chem (1999) 3.35
Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2. Proc Natl Acad Sci U S A (1998) 3.34
Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins (1988) 3.30
Graded changes in dose of a Xenopus activin A homologue elicit stepwise transitions in embryonic cell fate. Nature (1990) 3.27
Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell (2001) 3.25
Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. Biophys J (2000) 3.21
Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol (1994) 3.20
Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. J Mol Biol (1994) 3.16
Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins (1996) 3.14
Novel MRI contrast agent for molecular imaging of fibrin: implications for detecting vulnerable plaques. Circulation (2001) 3.12
Three key residues form a critical contact network in a protein folding transition state. Nature (2001) 3.09
Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys J (1997) 3.08
The human tumor cell-derived collagenase stimulatory factor (renamed EMMPRIN) is a member of the immunoglobulin superfamily. Cancer Res (1995) 3.04
The pathology of human aortic valve homografts. Thorax (1967) 3.01
The gene mutated in ataxia-ocular apraxia 1 encodes the new HIT/Zn-finger protein aprataxin. Nat Genet (2001) 3.01
Understanding beta-hairpin formation. Proc Natl Acad Sci U S A (1999) 3.01
Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol (1999) 2.99
The S receptor kinase determines self-incompatibility in Brassica stigma. Nature (2000) 2.96
Dynamical theory of activated processes in globular proteins. Proc Natl Acad Sci U S A (1982) 2.94
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci (1998) 2.94
Effective energy functions for protein structure prediction. Curr Opin Struct Biol (2000) 2.92
Hydrogen peroxide is involved in abscisic acid-induced stomatal closure in Vicia faba. Plant Physiol (2001) 2.91
Group II intron mobility occurs by target DNA-primed reverse transcription. Cell (1995) 2.86
The pathology of dry eye: the interaction between the ocular surface and lacrimal glands. Cornea (1998) 2.86
Lung cancer mortality and smoking habits: Mexican-American women. Am J Public Health (1982) 2.85
Plasma lipids and risk of developing renal dysfunction: the atherosclerosis risk in communities study. Kidney Int (2000) 2.85
Solvent mobility and the protein 'glass' transition. Nat Struct Biol (2000) 2.83
Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc Natl Acad Sci U S A (1994) 2.81
DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression. J Virol (1999) 2.80
The hinge-bending mode in lysozyme. Nature (1976) 2.78
Models of respiratory rhythm generation in the pre-Bötzinger complex. I. Bursting pacemaker neurons. J Neurophysiol (1999) 2.76
Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction. Development (1999) 2.76
The London Position Statement of the World Congress of Gastroenterology on Biological Therapy for IBD with the European Crohn's and Colitis Organization: when to start, when to stop, which drug to choose, and how to predict response? Am J Gastroenterol (2010) 2.74
Drosophila CtBP: a Hairy-interacting protein required for embryonic segmentation and hairy-mediated transcriptional repression. EMBO J (1998) 2.74
Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci (2000) 2.73
Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex. Neuron (1998) 2.73
Nucleotide sequence, transcription map, and mutation analysis of the 13q14 chromosomal region deleted in B-cell chronic lymphocytic leukemia. Blood (2001) 2.73
Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science (1989) 2.72
Direct ligand-receptor complex interaction controls Brassica self-incompatibility. Nature (2001) 2.69
The prevalence of NIDDM and associated risk factors in native Canadians. Diabetes Care (1997) 2.68
Pregnancy outcomes after kidney donation. Am J Transplant (2009) 2.66
Molecular dynamics simulations of the gramicidin channel. Annu Rev Biophys Biomol Struct (1994) 2.65
An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol (1984) 2.64
Neurofilament architecture combines structural principles of intermediate filaments with carboxy-terminal extensions increasing in size between triplet proteins. EMBO J (1983) 2.64
High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure (1997) 2.64