(Q26863623)

22

0 references

Ivet Bahar

3

Ivet Bahar

0 references

Kimmen Sjölander

27

Kimmen Sjölander

0 references

Mark Holder

Mark T. Holder

15

0 references

Julian Echave

Julian Echave

10

0 references

Jesse D. Bloom

Jesse Bloom

5

0 references

Arne Elofsson

Arne Elofsson

11

0 references

Ugo Bastolla

Ugo Bastolla

4

0 references

David D. Pollock

David D. Pollock

21

0 references

Eugene I. Shakhnovich

26

Eugene Shakhnovich

1 reference

9

Nikolay V. Dokholyan

1 reference

2

Sarah A. Teichmann

1 reference

20

Tina Perica

1 reference

23

Lynne Regan

1 reference

25

Nimrod Rubinstein

1 reference

24

Andrew Roger

1 reference

David A. Liberles

1

1 reference

Lucy J. Colwell

7

1 reference

A. P. Jason de Koning

8

1 reference

Dietlind L. Gerloff

12

1 reference

Richard A. Goldstein

13

1 reference

Johan A. Grahnen

14

1 reference

Clemens Lakner

16

1 reference

Nicholas Lartillot

17

1 reference

Simon C. Lovell

18

1 reference

Gavin Naylor

19

1 reference

Kimmen Sjölander

27

1 reference

Shamil Sunyaev

28

1 reference

Ashley I. Teufel

29

1 reference

Jeffrey L. Thorne

30

1 reference

Joseph W. Thornton

31

1 reference

Daniel M. Weinreich

32

1 reference

Simon Whelan

33

1 reference

language of work or name

1 reference

June 2012

1 reference

1 reference

21

1 reference

issue

6

1 reference

page(s)

769-85

1 reference

Non-adaptive origins of interactome complexity

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

miRBase: tools for microRNA genomics

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

A genomic code for nucleosome positioning

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

An integrated view of protein evolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evolution of Circular Permutations in Multidomain Proteins

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Molecular origin of polyglutamine aggregation in neurodegenerative diseases

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Binding properties and evolution of homodimers in protein-protein interaction networks

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution.

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

On the probability of fixation of mutant genes in a population

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

How are model protein structures distributed in sequence space?

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

3D domain swapping: a mechanism for oligomer assembly

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

De novo protein design: fully automated sequence selection

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

An in vivo map of the yeast protein interactome

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Detecting positive and purifying selection at synonymous sites in yeast and worm

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Thermodynamics of neutral protein evolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Proteome organization in a genome-reduced bacterium

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Antisense transcription in the mammalian transcriptome

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Darwinian evolution can follow only very few mutational paths to fitter proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Codon usage and tRNA content in unicellular and multicellular organisms

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Amino acid coevolution induces an evolutionary Stokes shift.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Three-dimensional domain swapping in the protein structure space

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Measuring the distance between multiple sequence alignments.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The relationship between proteome size, structural disorder and organism complexity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Biophysical and structural considerations for protein sequence evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The dynamics and evolutionary potential of domain loss and emergence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Ortholog identification in the presence of domain architecture rearrangement

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Exploring the factors determining the dynamics of different protein folds

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Sequence space and the ongoing expansion of the protein universe

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Global dynamics of proteins: bridging between structure and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Statistical potentials for improved structurally constrained evolutionary models.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Trade-off between positive and negative design of protein stability: from lattice models to real proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Lineage-specific differences in the amino acid substitution process

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evidence for an ancient adaptive episode of convergent molecular evolution.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Coding-sequence determinants of gene expression in Escherichia coli

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The role of quaternary structure in (beta/alpha)(8)-barrel proteins: evolutionary happenstance or a higher level of structure-function relationships?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Comparison of molecular dynamics and superfamily spaces of protein domain deformation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The antisense transcriptomes of human cells

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Tight regulation of unstructured proteins: from transcript synthesis to protein degradation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The impact of the nucleosome code on protein-coding sequence evolution in yeast

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Just how versatile are domains?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Emergence of symmetry in homooligomeric biological assemblies.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Arrangements in the modular evolution of proteins.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Assembly reflects evolution of protein complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Molecular mechanisms of polypeptide aggregation in human diseases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Modeling backbone flexibility improves protein stability estimation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Robust protein protein interactions in crowded cellular environments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Specificity and evolvability in eukaryotic protein interaction networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

3D complex: a structural classification of protein complexes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evolutionary conservation of protein backbone flexibility.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Expansion of protein domain repeats

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Emergence of protein fold families through rational design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Assessing site-interdependent phylogenetic models of sequence evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Hearing silence: non-neutral evolution at synonymous sites in mammals

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Site-to-site variation of synonymous substitution rates

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

An analysis of core deformations in protein superfamilies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

The power of two: protein dimerization in biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Supra-domains: evolutionary units larger than single protein domains

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Protein evolution with dependence among codons due to tertiary structure.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Topological determinants of protein folding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Purifying and directional selection in overlapping prokaryotic genes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Why are proteins so robust to site mutations?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Optimal protein-folding codes from spin-glass theory

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Stability of proteins: small globular proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Alignment uncertainty and genomic analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Comparative molecular dynamics--similar folds and similar motions?

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

An evolutionary model for maximum likelihood alignment of DNA sequences

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Evolution of overlapping genes

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3403413

Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

31 May 2018

1 reference

Co-evolution is incompatible with the Markov assumption in phylogenetics.

21 January 2018

1 reference

Phylogenetic substitution models for detecting heterotachy during plastid evolution.

21 January 2018

1 reference

A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies.

21 January 2018

1 reference

A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames.

21 January 2018

1 reference

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

21 January 2018

1 reference

Uniting Alignments and Trees

21 January 2018

1 reference

Protein disorder in the centrosome correlates with complexity in cell types number

21 January 2018

1 reference

A simple definition of structural regions in proteins and its use in analyzing interface evolution.

21 January 2018

1 reference

A single disulfide bond differentiates aggregation pathways of beta2-microglobulin.

21 January 2018

1 reference

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

21 January 2018

1 reference

Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

21 January 2018

1 reference

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates

21 January 2018

1 reference

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection

21 January 2018

1 reference

Protein design: a perspective from simple tractable models.

21 January 2018

1 reference

21 January 2018

1 reference

Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily.

21 January 2018

1 reference

Neutral evolution of model proteins: diffusion in sequence space and overdispersion

21 January 2018

1 reference

Domain deletions and substitutions in the modular protein evolution

21 January 2018

1 reference

Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds

21 January 2018

1 reference

Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution

21 January 2018

1 reference

The architecture of the protein domain universe

21 January 2018

1 reference

Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion

21 January 2018

1 reference

Topological Determinants of Protein Domain Swapping

21 January 2018

1 reference

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

21 January 2018

1 reference

Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

21 January 2018

1 reference

Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins

21 January 2018

1 reference

Conserved residues and the mechanism of protein folding

21 January 2018

1 reference

Distribution of Indel lengths

21 January 2018

1 reference

12 December 2020

Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial

1 reference

12 December 2020

Convergent dynamics in the protease enzymatic superfamily

1 reference

12 December 2020

Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments

1 reference

12 December 2020

A perturbative view of protein structural variation

1 reference

12 December 2020

Site interdependence attributed to tertiary structure in amino acid sequence evolution

1 reference

12 December 2020

Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family

1 reference

12 December 2020

Evolutionary conservation of protein vibrational dynamics

1 reference

12 December 2020

Structural constraints and emergence of sequence patterns in protein evolution

1 reference

12 December 2020

Why are proteins marginally stable?

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.2071

1 reference

681409

681409

1 reference

1 reference

1 reference