(Q36967996)

17 August 2017

Evolutionary trace for prediction and redesign of protein functional sites (English)

1 reference

17 August 2017

2

1 reference

17 August 2017

4

Olivier Lichtarge

1 reference

17 August 2017

Angela Wilkins

1

1 reference

17 August 2017

Rhonald Lua

series ordinal

3

1 reference

17 August 2017

language of work or name

English

0 references

publication date

1 January 2012

1 reference

Methods in Molecular Biology

17 August 2017

1 reference

17 August 2017

819

1 reference

17 August 2017

29-42

1 reference

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Role for the regulator of G-protein signaling homology domain of G protein-coupled receptor kinases 5 and 6 in beta 2-adrenergic receptor and rhodopsin phosphorylation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolutionary trace annotation of protein function in the structural proteome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

FLORA: a novel method to predict protein function from structure in diverse superfamilies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Identification of functionally important residues/domains in membrane proteins using an evolutionary approach coupled with systematic mutational analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Inference of macromolecular assemblies from crystalline state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

ET viewer: an application for predicting and visualizing functional sites in protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolutionary trace report_maker: a new type of service for comparative analysis of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis Strain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

A family of evolution-entropy hybrid methods for ranking protein residues by importance.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Combining inference from evolution and geometric probability in protein structure evaluation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Prediction and confirmation of a site critical for effector regulation of RGS domain activity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Gene ontology: tool for the unification of biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

A regulator of G protein signaling interaction surface linked to effector specificity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

29 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

An evolutionary trace method defines binding surfaces common to protein families

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Basic local alignment search tool

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Information-theoretical entropy as a measure of sequence variability

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Automated discovery of 3D motifs for protein function annotation

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolution of neural precursor selection: functional divergence of proneural proteins

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Identification of functional surfaces of the zinc binding domains of intracellular receptors

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4892863

An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22183528

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22183528

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structural clusters of evolutionary trace residues are statistically significant and common in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22183528

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/978-1-61779-465-0_3

1 reference

17 August 2017

1 reference

17 August 2017

PubMed publication ID

22183528

1 reference