(Q33748768)

29 July 2017

title

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster (English)

1 reference

29 July 2017

3

Haruki Nakamura

1 reference

29 July 2017

Jinzen Ikebe

1

0 references

author name string

Daron M Standley

series ordinal

2

1 reference

29 July 2017

Junichi Higo

series ordinal

4

1 reference

29 July 2017

publication date

1 January 2011

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29 July 2017

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29 July 2017

volume

20

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29 July 2017

issue

1

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29 July 2017

page(s)

187-196

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Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

ASH structure alignment package: sensitivity and selectivity in domain classification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Effects of solvent on the structure of the Alzheimer amyloid-beta(25-35) peptide

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Free‐energy landscape of a chameleon sequence in explicit water and its inherent α/β bifacial property

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

A global representation of the protein fold space

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Conformational transition states of a beta-hairpin peptide between the ordered and disordered conformations in explicit water

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Generalized-ensemble algorithms for molecular simulations of biopolymers

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Structural analysis of multifunctional peptide motifs in human bifunctional tRNA synthetase: identification of RNA-binding residues and functional implications for tandem repeats

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Generalized born models of macromolecular solvation effects

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Principles that govern the folding of protein chains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Conformational preferences of amino acids in globular proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047075

Replica-exchange molecular dynamics method for protein folding

28 July 2018

1 reference

The structure of the Alzheimer amyloid beta 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent.

21 January 2018

1 reference

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

21 January 2018

1 reference

beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain

21 January 2018

1 reference

Implicit solvation based on generalized Born theory in different dielectric environments

21 January 2018

1 reference

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.

21 January 2018

1 reference

Detecting local structural similarity in proteins by maximizing number of equivalent residues.

21 January 2018

1 reference

Simple but predictive protein models

21 January 2018

1 reference

Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble

21 January 2018

1 reference

Potentials of mean force between ionizable amino acid side chains in water

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21082745

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.553

1 reference

29 July 2017

1 reference

29 July 2017

1 reference