The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design (Q30389150)

17 August 2017

The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design (English)

1 reference

17 August 2017

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1 reference

2

Clare-Louise Towse

0 references

Valerie Daggett

series ordinal

3

object named as

Valerie Daggett

1 reference

PMC publication ID

4917059

17 August 2017

Matthew Carter Childers

object named as

Matthew Carter Childers

series ordinal

1

0 references

language of work or name

1 reference

9 June 2016

1 reference

Protein Engineering Design and Selection

17 August 2017

1 reference

17 August 2017

29

1 reference

17 August 2017

7

1 reference

17 August 2017

271-280

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The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Critical Assessment of Current Force Fields. Short Peptide Test Case

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

LoopIng: a template-based tool for predicting the structure of protein loops

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Local order in the unfolded state: conformational biases and nearest neighbor interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Unfolding studies of the cysteine protease baupain, a papain-like enzyme from leaves of Bauhinia forficata: effect of pH, guanidine hydrochloride and temperature.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Unusual biophysics of intrinsically disordered proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Mutational Tipping Points for Switching Protein Folds and Functions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Residual structure in unfolded proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

SHIFTX2: significantly improved protein chemical shift prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Sequence-Specific Random Coil Chemical Shifts of Intrinsically Disordered Proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Dynameomics: large-scale assessment of native protein flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Are current molecular dynamics force fields too helical?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

High-resolution design of a protein loop

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Intrinsic backbone preferences are fully present in blocked amino acids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Influence of denatured and intermediate states of folding on protein aggregation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDB.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Stereochemistry of polypeptide chain configurations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Modeling of loops in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

The "random-coil" state of proteins: comparison of database statistics and molecular simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Toward solving the folding pathway of barnase: the complete backbone 13C, 15N, and 1H NMR assignments of its pH-denatured state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Denatured states of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4917059

Thermal induced unfolding of human serum albumin isomers: assigning residual α helices to domain II.

20 June 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Urea-mediated protein denaturation: a consensus view

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Aromatic residues link binding and function of intrinsically disordered proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Conformational properties of a peptide model for unfolded alpha-helices

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Solvent sensitivity of protein unfolding: dynamical study of chicken villin headpiece subdomain in water-ethanol binary mixture.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Decoding the Mobility and Time Scales of Protein Loops

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

The denatured state ensemble contains significant local and long-range structure under native conditions: analysis of the N-terminal domain of ribosomal protein L9.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

The amide III vibrational circular dichroism band as a probe to detect conformational preferences of alanine dipeptide in water

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

A survey of left-handed helices in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Point mutations in protein globular domains: contributions from function, stability and misfolding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Toward better refinement of comparative models: predicting loops in inexact environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Revisiting the Ramachandran plot from a new angle

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/PROTEIN/GZW023

Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa

21 January 2018

1 reference

12 December 2020

Entropy reduction in unfolded peptides (and proteins) due to conformational preferences of amino acid residues

1 reference

12 December 2020

Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting

1 reference

12 December 2020

Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels

1 reference

12 December 2020

Identifiers

DOI

10.1093/PROTEIN/GZW023

1 reference

17 August 2017

1 reference

PMC publication ID

4917059

17 August 2017

PubMed publication ID

27284086

1 reference

PMC publication ID

4917059