(Q30009132)

21 May 2017

title

Constructing sequence-dependent protein models using coevolutionary information (English)

1 reference

21 May 2017

0 references

4

José N Onuchic

1 reference

21 May 2017

Ryan R Cheng

1

1 reference

21 May 2017

Mohit Raghunathan

series ordinal

2

1 reference

21 May 2017

Jeffrey K Noel

series ordinal

3

1 reference

21 May 2017

publication date

30 July 2015

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21 May 2017

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21 May 2017

volume

25

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21 May 2017

issue

1

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21 May 2017

page(s)

111-122

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UniProt: a hub for protein information

21 May 2017

cites work

1 reference

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22 May 2017

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The dominant folding route minimizes backbone distortion in SH3.

22 May 2017

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Protein structure prediction from sequence variation

22 May 2017

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Direct-coupling analysis of residue coevolution captures native contacts across many protein families

22 May 2017

1 reference

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Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks

22 May 2017

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Identification of direct residue contacts in protein-protein interaction by message passing

22 May 2017

1 reference

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Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

22 May 2017

1 reference

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Weak pairwise correlations imply strongly correlated network states in a neural population

22 May 2017

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GROMACS: fast, flexible, and free

22 May 2017

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22 May 2017

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Three-dimensional structure of the tyrosine kinase c-Src

22 May 2017

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Crystal structure of the ribosomal protein S6 from Thermus thermophilus

22 May 2017

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Toward an outline of the topography of a realistic protein-folding funnel

22 May 2017

1 reference

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

22 May 2017

1 reference

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The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

22 May 2017

1 reference

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A many-body term improves the accuracy of effective potentials based on protein coevolutionary data

22 May 2017

1 reference

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Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins

3 June 2018

1 reference

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Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding

3 June 2018

1 reference

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Evolution, energy landscapes and the paradoxes of protein folding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Learning To Fold Proteins Using Energy Landscape Theory.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Biophysics of protein evolution and evolutionary protein biophysics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Predictive energy landscapes for folding α-helical transmembrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Coevolutionary signals across protein lineages help capture multiple protein conformations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

The network of stabilizing contacts in proteins studied by coevolutionary data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Emerging methods in protein co-evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Predictive energy landscapes for protein-protein association

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Biomolecular dynamics: order-disorder transitions and energy landscapes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Statistical mechanics for natural flocks of birds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

High-resolution protein complexes from integrating genomic information with molecular simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Identification of the minimal protein-folding nucleus through loop-entropy perturbations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Transition states for folding of circular-permuted proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

The effects of nonnative interactions on protein folding rates: theory and simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Simulation, experiment, and evolution: understanding nucleation in protein S6 folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Theory of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Long-range order in the src SH3 folding transition state

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Experiment and theory highlight role of native state topology in SH3 folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Theory of protein folding: the energy landscape perspective

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Spin glasses and the statistical mechanics of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

3 June 2018

1 reference

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

21 January 2018

1 reference

21 January 2018

1 reference

Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model

21 January 2018

1 reference

Robustness and generalization of structure-based models for protein folding and function.

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

21 January 2018

1 reference

Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state

21 January 2018

1 reference

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

21 January 2018

1 reference

Complete change of the protein folding transition state upon circular permutation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815312

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26223372

12 December 2020

inferred from PubMed ID database lookup

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26223372

12 December 2020

inferred from PubMed ID database lookup

From structure to function: the convergence of structure based models and co-evolutionary information

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26223372

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1002/PRO.2758

1 reference

release_addkoo3jafagxjt7xiuhrvypve

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/addkoo3jafagxjt7xiuhrvypve

24 November 2022

mapped directly with Wikidata item

1 reference

1 reference

1 reference