Published in Biochemistry on May 11, 1982
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1983) 5.27
Accurate simulation of protein dynamics in solution. Proc Natl Acad Sci U S A (1988) 2.28
Protein hydration elucidated by molecular dynamics simulation. Proc Natl Acad Sci U S A (1993) 2.26
Biomolecule analysis by ion mobility spectrometry. Annu Rev Anal Chem (Palo Alto Calif) (2008) 1.89
Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. Proc Natl Acad Sci U S A (1983) 1.69
Atomic-level accuracy in simulations of large protein crystals. Proc Natl Acad Sci U S A (1994) 1.24
High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol (2006) 1.13
Molecular dynamics of myoglobin at 298 degrees K. Results from a 300-ps computer simulation. Biophys J (1985) 1.08
Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions. Protein Sci (2001) 0.93
Molecular dynamics of tryptophan in ribonuclease-T1. I. Simulation strategies and fluorescence anisotropy decay. Biophys J (1988) 0.93
Enhanced resolution of fluorescence anisotropy decays by simultaneous analysis of progressively quenched samples. Applications to anisotropic rotations and to protein dynamics. Biophys J (1987) 0.91
Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin. Biophys J (1994) 0.90
Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol (2016) 0.87
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophys J (2008) 0.86
A practical implicit solvent potential for NMR structure calculation. J Magn Reson (2014) 0.85
Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. J Comput Aided Mol Des (1997) 0.78
Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics. J Phys Chem B (2014) 0.77
All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Crystallographic R factor refinement by molecular dynamics. Science (1987) 15.90
Effective energy function for proteins in solution. Proteins (1999) 9.44
Dynamics of folded proteins. Nature (1977) 7.82
How does a protein fold? Nature (1994) 7.55
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
pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry (1990) 5.92
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1983) 5.27
Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science (1987) 4.89
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
Protein-folding dynamics. Nature (1976) 4.11
"New view" of protein folding reconciled with the old through multiple unfolding simulations. Science (1997) 3.93
X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution. J Mol Biol (1986) 3.49
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
Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins (1988) 3.30
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
Three key residues form a critical contact network in a protein folding transition state. Nature (2001) 3.09
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
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
Solvent mobility and the protein 'glass' transition. Nat Struct Biol (2000) 2.83
The hinge-bending mode in lysozyme. Nature (1976) 2.78
Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci (2000) 2.73
Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science (1989) 2.72
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
Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Biol (1999) 2.61
Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science (1990) 2.60
Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc Natl Acad Sci U S A (1985) 2.58
Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. Biochemistry (1979) 2.57
Local elevation: a method for improving the searching properties of molecular dynamics simulation. J Comput Aided Mol Des (1994) 2.54
Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers (1987) 2.53
Reversible peptide folding in solution by molecular dynamics simulation. J Mol Biol (1998) 2.48
The contribution of vibrational entropy to molecular association. The dimerization of insulin. J Mol Biol (1994) 2.45
Small-world view of the amino acids that play a key role in protein folding. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.43
Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers (1985) 2.43
Interpreting the folding kinetics of helical proteins. Nature (1999) 2.39
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J Mol Biol (1995) 2.39
Calculation of pi-pi excited state conformations and vibronic structure of retinal and related molecules. J Am Chem Soc (1974) 2.36
Thermal expansion of a protein. Biochemistry (1987) 2.25
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins (1999) 2.25
Early postnatal dexamethasone treatment and increased incidence of cerebral palsy. Arch Dis Child Fetal Neonatal Ed (2000) 2.24
Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc Natl Acad Sci U S A (2000) 2.24
Protein secondary structure prediction with a neural network. Proc Natl Acad Sci U S A (1989) 2.21
A dynamic model for the allosteric mechanism of GroEL. J Mol Biol (2000) 2.20
Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. J Mol Biol (1986) 2.16
Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A (1975) 2.14
A mathematical model for structure-function relations in hemoglobin. J Mol Biol (1972) 2.10
Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins (1991) 2.08
Dynamics of DNA oligomers. J Biomol Struct Dyn (1983) 2.08
The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc Natl Acad Sci U S A (1998) 2.07
The fundamentals of protein folding: bringing together theory and experiment. Curr Opin Struct Biol (1999) 2.05
Domain association in immunoglobulin molecules. The packing of variable domains. J Mol Biol (1985) 2.03
Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. J Mol Biol (1994) 1.97
Protein structural fluctuations during a period of 100 ps. Nature (1979) 1.96
Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc Natl Acad Sci U S A (1997) 1.95
Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study. Biochemistry (1983) 1.93
Folding thermodynamics of a model three-helix-bundle protein. Proc Natl Acad Sci U S A (1997) 1.89
Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior. Proc Natl Acad Sci U S A (1982) 1.89
Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J Mol Biol (1993) 1.88
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol (1998) 1.85
Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys J (1995) 1.83
Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra. Proc Natl Acad Sci U S A (1990) 1.82
Mechanism of tertiary structural change in hemoglobin. Proc Natl Acad Sci U S A (1977) 1.82
Electronic structure of cyanide complexes of hemes and heme proteins. J Mol Biol (1971) 1.79
Crystal structures of two closely related but antigenically distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes. J Immunol (2001) 1.77
Uracil-DNA glycosylase acts by substrate autocatalysis. Nature (2001) 1.77
Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci U S A (1994) 1.76
Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme. J Biomol NMR (2004) 1.76
Hemoglobin tertiary structural change on ligand binding. Its role in the co-operative mechanism. J Mol Biol (1983) 1.73
Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol (2002) 1.72
Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins (1995) 1.72
Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin. Science (1991) 1.70
Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. Proc Natl Acad Sci U S A (1983) 1.69
Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state. J Mol Biol (1999) 1.68
Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry (1991) 1.66
PDB-based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol (1997) 1.65
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. J Biomol NMR (2001) 1.65
Active site dynamics of ribonuclease. Proc Natl Acad Sci U S A (1985) 1.65
Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway. Biochemistry (1991) 1.64
Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Adv Protein Chem (1995) 1.63
Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior. Proteins (2001) 1.63
A protein structure from nuclear magnetic resonance data. lac repressor headpiece. J Mol Biol (1985) 1.62
Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. J Mol Biol (1995) 1.60
Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J Mol Biol (1981) 1.60
Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J Mol Biol (1997) 1.60
Clitoral and penile sizes of full term newborns in two different ethnic groups. J Pediatr Endocrinol Metab (1997) 1.60
The normal modes of the gramicidin-A dimer channel. Biophys J (1988) 1.59
Model for the structure of the lipid bilayer. Proc Natl Acad Sci U S A (1991) 1.58
Translational and rotational diffusion of proteins. J Mol Biol (1994) 1.56