(Q30361131)

14 October 2017

The evolution of protein structures and structural ensembles under functional constraint. (English)

1 reference

14 October 2017

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Jessica Siltberg-Liberles

series ordinal

1

1 reference

14 October 2017

Johan A Grahnen

series ordinal

2

1 reference

14 October 2017

David A Liberles

series ordinal

3

1 reference

14 October 2017

28 October 2011

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14 October 2017

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14 October 2017

2

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14 October 2017

4

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14 October 2017

748-762

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Creative Commons Attribution 4.0 International

14 October 2017

start time

28 October 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Biophysical and structural considerations for protein sequence evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Maps of protein structure space reveal a fundamental relationship between protein structure and function

3 June 2018

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Markov models of amino acid substitution to study proteins with intrinsically disordered regions

3 June 2018

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A biophysical protein folding model accounts for most mutational fitness effects in viruses

3 June 2018

1 reference

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Non-adaptive origins of interactome complexity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

The relationship between relative solvent accessibility and evolutionary rate in protein 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=3927589

Experimental illumination of a fitness landscape

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Exploring the factors determining the dynamics of different protein folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Quantifying the impact of dependent evolution among sites in phylogenetic inference

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Mutational effects and the evolution of new protein functions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Sequence space and the ongoing expansion of the protein universe

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Statistical potentials for improved structurally constrained evolutionary 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=3927589

The protein kingdom extended: ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Posttranslational regulation impacts the fate of duplicated genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Comparing models of evolution for ordered and disordered 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=3927589

The Pfam protein families database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

A sequence-compatible amount of native burial information is sufficient for determining the structure of 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=3927589

The continuity of protein structure space is an intrinsic property of 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=3927589

Physicochemical principles that regulate the competition between functional and dysfunctional association of 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=3927589

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

The effect of sequence evolution on protein structural divergence.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

The unfoldomics decade: an update on intrinsically disordered 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=3927589

Evaluating and optimizing computational protein design force fields using fixed composition-based negative 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=3927589

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence 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=3927589

The protein folding problem

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

How protein stability and new functions trade off

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

The structure of protein evolution and the evolution of protein structure.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Data growth and its impact on the SCOP database: new developments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Network analysis of protein dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

The frailty of adaptive hypotheses for the origins of organismal complexity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

A "silent" polymorphism in the MDR1 gene changes substrate specificity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Recent successes of the energy landscape theory of protein folding and function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Emergence of protein fold families through rational 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=3927589

Evaluation of models for the evolution of protein sequences and functions under structural constraint

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

A systematic search for positive selection in higher plants (Embryophytes)

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Evolution of Circular Permutations in Multidomain 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=3927589

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Specificity versus stability in computational protein 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=3927589

Physics and evolution of thermophilic adaptation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Functional coverage of the human genome by existing structures, structural genomics targets, and homology 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=3927589

Missense meanderings in sequence space: a biophysical view of protein 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=3927589

Structural disorder throws new light on moonlighting

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Protein structure and evolutionary history determine sequence space topology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

The family feud: do proteins with similar structures fold via the same pathway?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Global mapping of the protein structure space and application in structure-based inference of protein function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Heterotachy and functional shift in protein 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=3927589

The CATH database: an extended protein family resource for structural and functional genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Why are proteins so robust to site mutations?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Evolutionarily conserved pathways of energetic connectivity in protein families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

On the possibility of constructive neutral 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=3927589

Contact order, transition state placement and the refolding rates of single domain 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=3927589

Transmuting alpha helices and beta sheets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

Development of Neutral and Nearly Neutral Theories

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3927589

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=3927589

Evolution of structurally disordered proteins promotes neostructuralization

3 June 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

The evolution and evolutionary consequences of marginal thermostability in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

Mutational robustness of ribosomal protein genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

The folding and evolution of multidomain proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

Site-specific unfolding thermodynamics of a helix-turn-helix protein

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

Folding mechanism of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus: a test of the conservation of folding mechanisms hypothesis in (beta(alpha))(8) barrels

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

An insight into domain combinations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

Evolutionary rate heterogeneity in proteins with long disordered regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FGENES2040748

Intrinsic protein disorder in complete genomes

21 January 2018

1 reference

12 December 2020

A perturbative view of protein structural variation

1 reference

12 December 2020

Evolutionary conservation and variation of protein folding pathways. Two protease inhibitor homologues from black mamba venom

1 reference

12 December 2020

Evolutionary conservation of protein vibrational dynamics

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

Why are proteins marginally stable?

1 reference

12 December 2020

Identifiers

DOI

10.3390/GENES2040748

1 reference

14 October 2017

1 reference

14 October 2017

PubMed publication ID

24710290

1 reference