(Q39653480)

13 September 2017

Folding simulations of alanine-based peptides with lysine residues (English)

1 reference

13 September 2017

Sung SS

1

1 reference

PMCID

1281807

13 September 2017

language of work or name

English

0 references

publication date

1 March 1995

1 reference

13 September 2017

1 reference

13 September 2017

68

1 reference

13 September 2017

826-834

1 reference

13 September 2017

3

1 reference

Analytical approximation to the accessible surface area of proteins.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Helix folding simulations with various initial conformations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Solvation energy in protein folding and binding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Monte Carlo simulations of the folding of beta-barrel globular proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Unusually stable helix formation in short alanine-based peptides

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Monte Carlo simulation of equilibrium globular protein folding: alpha-helical bundles with long loops

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Dominant forces in protein folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Prediction of the thermodynamics of protein unfolding: the helix-coil transition of poly(L-alanine).

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Polymer principles in protein structure and stability.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Electrostatic Energy and Macromolecular Function

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

The mechanism of alpha-helix formation by peptides

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

The intrinsic helix-forming tendency of L-alanine

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

A simplified representation of protein conformations for rapid simulation of protein folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Local interactions in bends of proteins

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Molecular mechanics in biology: from structure to function, taking account of solvation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Hydrogen bonding, hydrophobicity, packing, and protein folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Realistic simulations of native-protein dynamics in solution and beyond

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Attractive forces between uncharged hydrophobic surfaces: direct measurements in aqueous solution.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine).

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Voiding dysfunction in patients with human T-lymphotropic virus type-1-associated myelopathy (HAM).

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Applications of simulated annealing to peptides.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Large differences in the helix propensities of alanine and glycine

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Molecular dynamics simulations of helix denaturation

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Short alanine-based peptides may form 3(10)-helices and not alpha-helices in aqueous solution

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Long-range surface charge-charge interactions in proteins. Comparison of experimental results with calculations from a theoretical method.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Volume changes in protein evolution.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Helix-forming tendencies of nonpolar amino acids predicted by Monte Carlo simulated annealing

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1281807

Prediction of the folding of short polypeptide segments by uniform conformational sampling

2 December 2018

1 reference

12 December 2020

Water-inserted alpha-helical segments implicate reverse turns as folding intermediates

1 reference

12 December 2020

1 reference

12 December 2020

The inclusion of electrostatic hydration energies in molecular mechanics calculations

1 reference

12 December 2020

Molecular dynamics of native protein. I. Computer simulation of trajectories

1 reference

12 December 2020

Van der waals picture of liquids, solids, and phase transformations

1 reference

12 December 2020

Intermolecular Forces and the Nature of the Liquid State: Liquids reflect in their bulk properties the attractions and repulsions of their constituent molecules

1 reference

12 December 2020

The hydrophobic interaction is long range, decaying exponentially with distance

1 reference

12 December 2020

10.1016/S0006-3495(95)80259-6

Identifiers

DOI

1 reference

13 September 2017

1 reference

13 September 2017

1 reference

PMCID

1281807