Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations

scientific article

Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1110/PS.44901
P932PMC publication ID2374007
P698PubMed publication ID11369854
P5875ResearchGate publication ID11968094

P2093author name stringH Nakamura
N Nakajima
S Ono
N Ito
M Kuroda
J Higo
P2860cites workMulticanonical ensemble: A new approach to simulate first-order phase transitionsQ21698968
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Analysis of long-range interactions in a model denatured state of staphylococcal nuclease based on correlated changes in backbone dynamicsQ30175738
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Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleusQ73329892
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Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structuresQ73335305
Protein dynamics determined by backbone conformation and atom packingQ73439303
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulationsQ74452346
Monte Carlo simulation and global optimization without parametersQ74555822
Origin of the designability of protein structuresQ77993695
Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in foldingQ33179891
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathwayQ33702131
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein GQ33845595
Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptideQ33877281
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.Q34481107
Understanding beta-hairpin formationQ35594815
Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy.Q36279000
Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambinQ36280885
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The turn sequence directs beta-strand alignment in designed beta-hairpinsQ36281322
Folding of Protein G B1 Domain Studied by the Conformational Characterization of Fragments Comprising Its Secondary Structure ElementsQ36686880
Folding dynamics and mechanism of beta-hairpin formationQ36890665
Structural analysis of non-native states of proteins by NMR methodsQ41026035
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Protein folding in the landscape perspective: chevron plots and non-Arrhenius kineticsQ41690266
Simulations of protein folding and unfoldingQ44760159
Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozymeQ47624602
Native-like beta-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues.Q50537991
Free energy landscapes of peptides by enhanced conformational sampling.Q52082381
Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue.Q52082493
Molecular dynamics simulations of beta-hairpin folding.Q52133674
Lattice simulations of aggregation funnels for protein folding.Q52208610
Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.Q52242026
Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide.Q52306978
New Monte Carlo algorithm: Entropic sampling.Q52393347
"New view" of protein folding reconciled with the old through multiple unfolding simulations.Q52528318
Replica-exchange molecular dynamics method for protein foldingQ55879366
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesQ55918670
Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential EnergyQ56093107
Emergence of Preferred Structures in a Simple Model of Protein FoldingQ56517454
Theory of the Phase Transition between Helix and Random Coil in Polypeptide ChainsQ56522033
NMR determination of residual structure in a urea-denatured protein, the 434-repressorQ57825884
Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella samplingQ57828897
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformationsQ57828939
Multidimensional replica-exchange method for free-energy calculationsQ57906232
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscapeQ57906240
Generalized-ensemble Monte Carlo method for systems with rough energy landscapeQ57906304
Numerical comparisons of three recently proposed algorithms in the protein folding problemQ57906307
Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensembleQ57906319
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problemQ57906365
Folding-unfolding thermodynamics of a ?-heptapeptide from equilibrium simulationsQ58616280
An Analysis on Protein Folding Problem by Replica-Exchange MethodQ62846791
De novo design and structural analysis of a model beta-hairpin peptide systemQ71169131
A microscopic view of helix propagation: N and C-terminal helix growth in alanine helicesQ71176299
Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly beta-sheet proteinQ71604199
P433issue6
P407language of work or nameEnglishQ1860
P921main subjectenergy landscapeQ5377166
helical hairpinQ60761532
P304page(s)1160-71
P577publication date2001-06-01
P1433published inProtein ScienceQ7251445
P1476titleEnergy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations
P478volume10

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