Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins (Q40650676)

22 September 2017

Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins (English)

1 reference

22 September 2017

0 references

Masanari Matsuoka

1 reference

22 September 2017

Takeshi Kikuchi

series ordinal

1 reference

22 September 2017

23 May 2014

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22 September 2017

BMC Structural Biology

1 reference

22 September 2017

1 reference

22 September 2017

1 reference

Funneling and frustration in the energy landscapes of some designed and simplified proteins.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Positively selected sites in cetacean myoglobins contribute to protein stability

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

The protein-folding problem, 50 years on.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Protein structural modularity and robustness are associated with evolvability.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Analyses of Protein Sequences Using Inter-Residue Average Distance Statistics to Study Folding Processes and the Significance of Their Partial Sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

What lessons can be learned from studying the folding of homologous proteins?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

SeqRate: sequence-based protein folding type classification and rates prediction

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Coevolution of function and the folding landscape: correlation with density of native contacts

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

PAML 4: phylogenetic analysis by maximum likelihood

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Malleability of protein folding pathways: a simple reason for complex behaviour

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

In quest of an empirical potential for protein structure prediction.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Protein sequence entropy is closely related to packing density and hydrophobicity

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

MUSCLE: multiple sequence alignment with high accuracy and high throughput

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

NMR solution structure of the activation domain of human procarboxypeptidase A2

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Determination of a transition state at atomic resolution from protein engineering data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Mapping the folding pathway of an immunoglobulin domain: structural detail from Phi value analysis and movement of the transition state

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

From snapshot to movie: phi analysis of protein folding transition states taken one step further

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

VMD: visual molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Crystal structure of the ribosomal protein S6 from Thermus thermophilus

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

SCOP: a structural classification of proteins database for the investigation of sequences and structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Environment and exposure to solvent of protein atoms. Lysozyme and insulin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

The neighbor-joining method: a new method for reconstructing phylogenetic trees

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Prediction of the location of structural domains in globular proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Mapping the transition state and pathway of protein folding by protein engineering

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Basic local alignment search tool

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

The folding of hen lysozyme involves partially structured intermediates and multiple pathways

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

The rapid generation of mutation data matrices from protein sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Three-dimensional structure of acylphosphatase. Refinement and structure analysis

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

The Protein Data Bank: a computer-based archival file for macromolecular structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Conservation of folding pathways in evolutionarily distant globin sequences

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Analyses of the folding properties of ferredoxin-like fold proteins by means of a coarse-grained Gō model: relationship between the free energy profiles and folding cores.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Relationship between protein folding kinetics and amino acid properties

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Predicting protein folding rate from amino acid sequence

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Global and local prediction of protein folding rates based on sequence autocorrelation information

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Subdomain competition, cooperativity, and topological frustration in the folding of CheY.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

The folding process of acylphosphatase from Escherichia coli is remarkably accelerated by the presence of a disulfide bond.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Direct correlation between proteins' folding rates and their amino acid compositions: an ab initio folding rate prediction

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Amino acid sequence predicts folding rate for middle-size two-state proteins

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Prediction of folding pathway and kinetics among plant hemoglobins using an average distance map method.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Analysis of the differences in the folding kinetics of structurally homologous proteins based on predictions of the gross features of residue contacts

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Folding and aggregation are selectively influenced by the conformational preferences of the alpha-helices of muscle acylphosphatase.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Evolutionary conservation of the folding nucleus.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4055915

Effect of H helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin 1 1Edited by F. Cohen

19 August 2018

1 reference

https://api.crossref.org/works/10.1186%2F1472-6807-14-15

A breakdown of symmetry in the folding transition state of protein L

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1472-6807-14-15

Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1472-6807-14-15

Stabilisation of α-helices by site-directed mutagenesis reveals the importance of secondary structure in the transition state for acylphosphatase folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1472-6807-14-15

Analysis of the differences in the folding mechanisms of c-type lysozymes based on contact maps constructed with interresidue average distances

21 January 2018

1 reference

12 December 2020

The nucleation mechanism of protein folding: a survey of computer simulation studies

1 reference

12 December 2020

Composition-based effective chain length for prediction of protein folding rates

1 reference

12 December 2020

Identifying a folding nucleus for the lysozyme/alpha-lactalbumin family from sequence conservation clusters

1 reference

12 December 2020

Non-functional conserved residues in globins and their possible role as a folding nucleus

1 reference

12 December 2020

Fast compaction of alpha-lactalbumin during folding studied by stopped-flow X-ray scattering

1 reference

12 December 2020

Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing

1 reference

12 December 2020

Folding mechanism of three structurally similar beta-sheet proteins

1 reference

12 December 2020

Different folding pathways taken by highly homologous proteins, goat alpha-lactalbumin and canine milk lysozyme

1 reference

12 December 2020

Changes of protein folding pathways by circular permutation. Overlapping nuclei promote global cooperativity

1 reference

12 December 2020

The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology

1 reference

12 December 2020

Identifiers

DOI

10.1186/1472-6807-14-15

1 reference

Dimensions Publication ID

22 September 2017

0 references

1 reference

22 September 2017

PubMed publication ID

24884463

1 reference