(Q34101699)

31 July 2017

Biophysical and structural considerations for protein sequence evolution (English)

1 reference

31 July 2017

0 references

Johan A Grahnen

1

1 reference

31 July 2017

Priyanka Nandakumar

series ordinal

2

1 reference

31 July 2017

Jan Kubelka

series ordinal

3

1 reference

31 July 2017

David A Liberles

series ordinal

4

1 reference

31 July 2017

16 December 2011

1 reference

31 July 2017

BMC Evolutionary Biology

1 reference

31 July 2017

11

1 reference

31 July 2017

361

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-11-361

31 July 2017

0 references

cites work

Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Equilibrium distribution from distributed computing (simulations of protein folding).

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Challenges in protein folding simulations: Timescale, representation, and analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Among-site rate variation and its impact on phylogenetic analyses

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Theoretical and computational protein design

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Quantifying the impact of dependent evolution among sites in phylogenetic inference

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Live imaging of single nuclear pores reveals unique assembly kinetics and mechanism in interphase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Mutational effects and the evolution of new protein functions.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Multiscale coarse-graining of the protein energy landscape

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Statistical potentials for improved structurally constrained evolutionary models.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Current status of the AMOEBA polarizable force field

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

The Pfam protein families database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

The SH2 domains of inositol polyphosphate 5-phosphatases SHIP1 and SHIP2 have similar ligand specificity but different binding kinetics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

INDELible: a flexible simulator of biological sequence evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Solvent accessible surface area approximations for rapid and accurate protein structure prediction.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

The protein folding problem

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Recent advances in implicit solvent-based methods for biomolecular simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Protein stability imposes limits on organism complexity and speed of molecular evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

A coarse-grained protein force field for folding and structure prediction.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Actin turnover-dependent fast dissociation of capping protein in the dendritic nucleation actin network: evidence of frequent filament severing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

ProtTest: selection of best-fit models of protein evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

WebLogo: A Sequence Logo Generator

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Simulating protein evolution in sequence and structure space

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Optimization of specificity in a cellular protein interaction network by negative selection

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

A graph-theory algorithm for rapid protein side-chain prediction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Heterotachy and functional shift in protein evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Predicting functional divergence in protein evolution by site-specific rate shifts

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Heterotachy, an important process of protein evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Correlation between the substitution rate and rate variation among sites in protein evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

A helix propensity scale based on experimental studies of peptides and proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

A new method for analyzing protein sequence relationships based on Sammon maps

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Development of Neutral and Nearly Neutral Theories

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Evolution of the Zfx and Zfy genes: rates and interdependence between the genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Knowledge-based potentials for proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Principles that govern the folding of protein chains

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Spin glasses and the statistical mechanics of protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

The evolution and evolutionary consequences of marginal thermostability in proteins.

28 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Optimizing potentials for the inverse protein folding problem.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

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/10.1186%2F1471-2148-11-361

Evolution of structurally disordered proteins promotes neostructuralization

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Missense meanderings in sequence space: a biophysical view of protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

The relationship between relative solvent accessibility and evolutionary rate in protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Comparative assessment of scoring functions on a diverse test set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

PepX: a structural database of non-redundant protein-peptide complexes

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

A residue-pairwise generalized born scheme suitable for protein design calculations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

Calculation of the dielectric properties of a protein and its solvent: theory and a case study

28 October 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3292521

28 October 2018

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-11-361

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22171550

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The activation of RalGDS can be achieved independently of its Ras binding domain. Implications of an activation mechanism in Ras effector specificity and signal distribution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22171550

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2148-11-361

1 reference

Dimensions Publication ID

31 July 2017

0 references

1 reference

31 July 2017

1 reference