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Protein dynamics in solution and in a crystalline environment: a molecular dynamics study
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Vibrational approach to the dynamics of an α‐helix
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A method for constrained energy minimization of macromolecules
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Dynamics of the aromatic amino acid residues in the globular conformation of the basic pancreatic trypsin inhibitor (BPTI)
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New method for searching for neighbors in molecular dynamics computations
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Quiet high-resolution computer models of a plasma
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Gene duplications in the structural evolution of chymotrypsin
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Fluorescence relaxation and correlation spectroscopy in the analysis of conformational dynamics
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The Basic Trypsin Inhibitor of Bovine Pancreas
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Some Factors in the Interpretation of Protein Denaturation
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Equilibrium structure and molecular motion in liquids
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Solvent viscosity and protein dynamics
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Picosecond dynamics of tyrosine side chains in proteins
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Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment
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Quenching of protein fluorescence by oxygen. Detection of structural fluctuations in proteins on the nanosecond time scale
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Monte Carlo calculations in the isothermal-isobaric ensemble. 2. Dilute aqueous solution of methane
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Solvation. A molecular dynamics study of a dipeptide in water
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Vibrational Analysis of Peptides, Polypeptides, and Proteins. 3. α-Poly(L-alanine)
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Computer simulation of the solvent structure around biological macromolecules
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Dynamic model of globular protein conformations based on NMR studies in solution
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Protein structural fluctuations during a period of 100 ps
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Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
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Crystallographic studies of the dynamic properties of lysozyme
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Molecular dynamics of ferrocytochrome c
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Internal mobility of ferrocytochrome c
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Molecular Dynamics Study of Temperature Effects on Water Structure and Kinetics
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Molecular dynamics study of the hydration of Lennard-Jones solutes
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Molecular dynamics of polymeric systems
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Brownian dynamics study of polymer conformational transitions
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Brownian dynamics study of a polymer chain of linked rigid bodies
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Molecular dynamics simulation of polymers. I. Structure
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A Monte Carlo simulation of the hydrophobic interaction
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Room Temperature Phosphorescence and the Dynamic Aspects of Protein Structure
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Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.
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Mechanism of tertiary structural change in hemoglobin.
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Dynamics of activated processes in globular proteins.
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Algorithms for macromolecular dynamics and constraint dynamics
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Constrained dynamics of flexible molecules
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Inelastic laser light scattering from synthetic and biological polymers
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Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
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Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution
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BREATHING MODE OF CONFORMATIONAL FLUCTUATIONS IN GLOBULAR PROTEINS
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AREAS, VOLUMES, PACKING, AND PROTEIN STRUCTURE
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Hydrogen Exchange Kinetics and Internal Motions in Proteins and Nucleic Acids
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X-ray Crystallographic Studies of Proteins
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Intermediate water structures in solution of alanine dipeptide
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Stochastic dynamic simulation of a protein
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Enhanced resolution of fluorescence anisotropy decays by simultaneous analysis of progressively quenched samples. Applications to anisotropic rotations and to protein dynamics
inferred← citeshttps://doi.org/10.1016/s0006-3495(88)82954-0openalex-snapshot
Molecular dynamics of tryptophan in ribonuclease-T1. I. Simulation strategies and fluorescence anisotropy decay
inferred← citeshttps://doi.org/10.1016/s0006-3495(94)80837-9openalex-snapshot
Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin
inferred← citeshttps://doi.org/10.1016/s0021-9258(18)66863-2openalex-snapshot
Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode.
inferred← citeshttps://doi.org/10.1016/s0022-2836(05)80156-1openalex-snapshot
The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water
inferred← citeshttps://doi.org/10.1016/s0022-2836(05)80196-2openalex-snapshot
Temperature dependence of the structure and dynamics of myoglobin
inferred← citeshttps://doi.org/10.1016/s0022-2836(05)80363-8openalex-snapshot
Temperature Dependence of dynamics of hydrated myoglobin
inferred← citeshttps://doi.org/10.1016/s0022-2836(83)80120-xopenalex-snapshot
Pancreatic trypsin inhibitor
inferred← citeshttps://doi.org/10.1016/s0022-2836(83)80304-0openalex-snapshot
Molecular dynamics of native protein
inferred← citeshttps://doi.org/10.1016/s0022-2836(83)80305-2openalex-snapshot
Integrating the equations of motion
inferred← citeshttps://doi.org/10.1016/s0022-2836(83)80306-4openalex-snapshot
Molecular dynamics of native protein
inferred← citeshttps://doi.org/10.1016/s0167-7306(08)60564-5openalex-snapshot
Chapter 5 Protein crystallography
inferred← citeshttps://doi.org/10.1016/s1044-0305(99)00026-4openalex-snapshot
Hydroiodic acid attachment kinetics as a chemical probe of gaseous protein ion structure: Bovine pancreatic trypsin inhibitor
inferred← citeshttps://doi.org/10.1017/s0033583500003723openalex-snapshot
Protein dynamics: comparison of simulations with inelastic neutron scattering experiments
inferred← citeshttps://doi.org/10.1017/s0033583500005217openalex-snapshot
Hydrogen exchange and structural dynamics of proteins and nucleic acids
inferred← citeshttps://doi.org/10.1021/ar00090a001openalex-snapshot
The dynamic picture of protein structure
inferred← citeshttps://doi.org/10.1021/ar960081xopenalex-snapshot
Unfolding, Refolding, and Hydration of Proteins in the Gas Phase
inferred← citeshttps://doi.org/10.1021/bi00281a017openalex-snapshot
Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study
inferred← citeshttps://doi.org/10.1021/bi00336a003openalex-snapshot
Vicinal coupling constants and protein dynamics
inferred← citeshttps://doi.org/10.1021/bi00375a012openalex-snapshot
Picosecond resolution of tyrosine fluorescence and anisotropy decays by 2-GHz frequency-domain fluorometry
inferred← citeshttps://doi.org/10.1021/bi00418a037openalex-snapshot
Dynamics simulation studies of apoazurin of Alcaligenes denitrificans
inferred← citeshttps://doi.org/10.1021/bi00422a026openalex-snapshot
Quenching of room temperature protein phosphorescence by added small molecules
inferred← citeshttps://doi.org/10.1021/bi00431a031openalex-snapshot
Proton magnetic resonance study of the influence of chemical modification, mutation, quaternary state, and ligation state on dynamic stability of the heme pocket in hemoglobin as reflected in the exchange of the proximal histidyl ring labile proton
inferred← citeshttps://doi.org/10.1021/ct700119mopenalex-snapshot
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
inferred← citeshttps://doi.org/10.1021/ct8003832openalex-snapshot
United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials
inferred← citeshttps://doi.org/10.1021/ie901909copenalex-snapshot
Molecular Modeling of Matter: Impact and Prospects in Engineering
inferred← citeshttps://doi.org/10.1021/ja951005copenalex-snapshot
Poly(oxyethylene)−Water Interactions: A Molecular Dynamics Study
inferred← citeshttps://doi.org/10.1021/ja960153fopenalex-snapshot
Solvation and Dynamics of Chymotrypsin in Hexane
inferred← citeshttps://doi.org/10.1021/ja9619059openalex-snapshot
Protein Structure in Vacuo: Gas-Phase Conformations of BPTI and Cytochrome c
inferred← citeshttps://doi.org/10.1021/ja962776zopenalex-snapshot
Structure and Dynamics of a Peptidoglycan Monomer in Aqueous Solution Using NMR Spectroscopy and Simulated Annealing Calculations
inferred← citeshttps://doi.org/10.1021/ja962914kopenalex-snapshot
Conformations, Unfolding, and Refolding of Apomyoglobin in Vacuum: An Activation Barrier for Gas-Phase Protein Folding
inferred← citeshttps://doi.org/10.1021/ja980324bopenalex-snapshot
Thermal Unfolding of Unsolvated Cytochrome c: Experiment and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/ja991309popenalex-snapshot
Internal and Overall Peptide Group Motion in Proteins: Molecular Dynamics Simulations for Lysozyme Compared with Results from X-ray and NMR Spectroscopy
inferred← citeshttps://doi.org/10.1021/jp065877kopenalex-snapshot
Molecular Dynamics Study on the Solvent Dependent Heme Cooling Following Ligand Photolysis in Carbonmonoxy Myoglobin
inferred← citeshttps://doi.org/10.1021/jp4124327openalex-snapshot
Aligning Experimental and Theoretical Anisotropic B-Factors: Water Models, Normal-Mode Analysis Methods, and Metrics
inferred← citeshttps://doi.org/10.1021/jp807499yopenalex-snapshot
Diversity of Solvent Dependent Energy Transfer Pathways in Heme Proteins
inferred← citeshttps://doi.org/10.1021/jp963389eopenalex-snapshot
Hydration of Gas Phase Proteins: Folded +5 and Unfolded +7 Charge States of Cytochrome c
inferred← citeshttps://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferred← citeshttps://doi.org/10.1023/a:1007919812771openalex-snapshot
Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein
inferred← citeshttps://doi.org/10.1038/71231openalex-snapshot
Solvent mobility and the protein 'glass' transition.
inferred← citeshttps://doi.org/10.1038/s41467-024-47473-4openalex-snapshot
Functional protein dynamics in a crystal
inferred← citeshttps://doi.org/10.1038/s41557-026-02155-0openalex-snapshot
Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes
inferred← citeshttps://doi.org/10.1063/1.445724openalex-snapshot
Deformable stochastic boundaries in molecular dynamics
inferred← citeshttps://doi.org/10.1063/1.458885openalex-snapshot
Inelastic neutron scattering analysis of low-frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor
inferred← citeshttps://doi.org/10.1063/1.466177openalex-snapshot
Molecular dynamics simulations of ring inversion in RDX
inferred← citeshttps://doi.org/10.1063/1.478887openalex-snapshot
Protein flexibility in solution and in crystals
inferred← citeshttps://doi.org/10.1073/pnas.80.14.4315openalex-snapshot
Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data.
inferred← citeshttps://doi.org/10.1073/pnas.80.21.6571openalex-snapshot
Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.
inferred← citeshttps://doi.org/10.1073/pnas.85.20.7557openalex-snapshot
Accurate simulation of protein dynamics in solution.
inferred← citeshttps://doi.org/10.1073/pnas.90.19.9135openalex-snapshot
Protein hydration elucidated by molecular dynamics simulation.
inferred← citeshttps://doi.org/10.1073/pnas.91.18.8715openalex-snapshot
Atomic-level accuracy in simulations of large protein crystals.
inferred← citeshttps://doi.org/10.1080/00268979400101331openalex-snapshot
A molecular dynamics simulation study of chloroform
inferred← citeshttps://doi.org/10.1080/07391102.1985.10507606openalex-snapshot
Monte Carlo Simulation of Myoglobin Primary to Helical Structure
inferred← citeshttps://doi.org/10.1080/07391102.1985.10508407openalex-snapshot
Solvent Structure and Enzyme Activity
inferred← citeshttps://doi.org/10.1080/07391102.1991.10507918openalex-snapshot
Molecular Dynamics Simulations of Dinucleoside and Dinucleoside-Drug Crystal Hydrates
inferred← citeshttps://doi.org/10.1080/08927029208022491openalex-snapshot
Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor
inferred← citeshttps://doi.org/10.1080/08927029508022326openalex-snapshot
Molecular Dynamics Simulations of Adsorbed Alkanes in Silica Micropores at Low-to-Moderate Loadings
inferred← citeshttps://doi.org/10.1088/1742-6596/46/1/047openalex-snapshot
Large-scale simulations of the ribosome: a new landmark in computational biology
inferred← citeshttps://doi.org/10.1101/2023.07.06.548023openalex-snapshot
Functional Protein Dynamics in a Crystal
inferred← citeshttps://doi.org/10.1107/s2052252522011198openalex-snapshot
Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
inferred← citeshttps://doi.org/10.1110/ps.800101openalex-snapshot
Enzyme specificity under dynamic control II: Principal component analysis of α‐lytic protease using global and local solvent boundary conditions
inferred← citeshttps://doi.org/10.1111/j.1432-1033.1993.tb17705.xopenalex-snapshot
The NMR solution structure of a Kunitz‐type proteinase inhibitor from the sea anemone Stichodactyla helianthus
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Structure/activity relationship of adenine‐modified NAD derivatives with respect to porcine heart lactate dehydrogenase isozyme H4 simulated with molecular mechanics
inferred← citeshttps://doi.org/10.1111/j.1749-6632.1985.tb25792.xopenalex-snapshot
Dynamic Aspects of Protein Structure
inferred← citeshttps://doi.org/10.1111/j.1749-6632.1986.tb20961.xopenalex-snapshot
Simulations of Proteins in Watera
inferred← citeshttps://doi.org/10.1142/s2010194512005259openalex-snapshot
PROTEIN STRUCTURE PREDICTION USING GAS PHASE MOLECULAR DYNAMICS SIMULATION: EOTAXIN-3 CYTOKINE AS A CASE STUDY
inferred← citeshttps://doi.org/10.1143/jpsj.52.4407openalex-snapshot
Conformational Flexibility of Bovine Pancreatic Ribonuclease A
inferred← citeshttps://doi.org/10.1146/annurev.anchem.1.031207.113001openalex-snapshot
Biomolecule Analysis by Ion Mobility Spectrometry
inferred← citeshttps://doi.org/10.1146/annurev.biophys.32.110601.142445openalex-snapshot
The Role of Dynamics in Enzyme Activity
inferred← citeshttps://doi.org/10.1529/biophysj.107.119115openalex-snapshot
Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics
inferred← citeshttps://doi.org/10.3390/e16010138openalex-snapshot
Time Integrators for Molecular Dynamics
inferred← citeshttps://doi.org/10.3390/molecules27020488openalex-snapshot
Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study
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Navigating the Intricacies of Molecular Docking
inferred← citeshttps://doi.org/10.48550/arxiv.1111.5468openalex-snapshot
Model for crankshaft motion of protein backbone in nonspecific binding site of serine proteases
inferred← citeshttps://doi.org/10.48550/arxiv.1309.5007openalex-snapshot
On Metropolis Integrators for Molecular Dynamics
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