(Q47714083)

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Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides (English)

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

Tobin R. Sosnick

5

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Tobin R Sosnick

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Europe PubMed Central

PubMed publication ID

5 February 2018

4

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Karl F Freed

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

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Muhammad H Zaman

1

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

Min-Yi Shen

2

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

R Stephen Berry

3

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

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1 August 2003

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

Journal of Molecular Biology

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

331

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

3

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

693-711

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Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

Conformation of Polypeptides and Proteins

1 reference

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Stereochemistry of polypeptide chain configurations

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Reaction coordinates of biomolecular isomerization

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Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

1 reference

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The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding

1 reference

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Entropic benefit of a cross-link in protein association

1 reference

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Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

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Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

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Polyproline II structure in a sequence of seven alanine residues.

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Is polyproline II a major backbone conformation in unfolded proteins?

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The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy.

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Docking enzyme-inhibitor complexes using a preference-based free-energy surface

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Reassessment of the random coil conformation: vibrational CD study of proline oligopeptides and related polypeptides

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Subpicosecond conformational dynamics of small peptides probed by two-dimensional vibrational spectroscopy

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Dihedral angles of tripeptides in solution directly determined by polarized Raman and FTIR spectroscopy

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Alpha-helix-forming propensities in peptides and proteins

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Absolute comparison of simulated and experimental protein-folding dynamics

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Native-like mean structure in the unfolded ensemble of small proteins

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The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

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All-atom fast protein folding simulations: the villin headpiece

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Molecular dynamics simulations of hydrophobic collapse of ubiquitin

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The dual role of a loop with low loop contact distance in folding and domain swapping

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Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding

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Molecular theory of the helix-coil transitionin in poly(amino acids). IV. Evaluation and analysis of s for poly(L-valine) in the absence and presence of water

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Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains

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Pathway diversity and concertedness in protein folding: an ab-initio approach.

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Energetic coupling between DNA bending and base pair opening

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Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

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Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

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Replica-exchange molecular dynamics method for protein folding

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Multidimensional replica-exchange method for free-energy calculations

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Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution

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Identifiers

10.1016/S0022-2836(03)00765-4

1 reference

Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

5 February 2018

http://europepmc.org/abstract/MED/12899838

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