(Q34283516)

1 August 2017

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

1 reference

1 August 2017

0 references

3

1 reference

1 August 2017

A D Wilkins

1

1 reference

1 August 2017

R Lua

series ordinal

2

1 reference

1 August 2017

R M Ward

series ordinal

4

1 reference

1 August 2017

O Lichtarge

series ordinal

5

1 reference

1 August 2017

1 July 2010

1 reference

1 August 2017

1 reference

1 August 2017

19

1 reference

1 August 2017

1296-1311

1 reference

1 August 2017

7

1 reference

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

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Evolutionary trace annotation of protein function in the structural proteome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Exploitation of binding energy for catalysis and design

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Protein sectors: evolutionary units of three-dimensional structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Protein promiscuity and its implications for biotechnology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

NMR structures of two designed proteins with high sequence identity but different fold and function

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Recombinant human growth hormone: rationale for use in the treatment of HIV-associated lipodystrophy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

De novo computational design of retro-aldol enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Rational design of competitive prolactin/growth hormone receptor antagonists

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Understanding the molecular machinery of genetics through 3D structures

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Predicting protein function from sequence and structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Essential helix interactions in the anion transporter domain of prestin revealed by evolutionary trace analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Rapid detection of similarity in protein structure and function through contact metric distances

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Searching for new allosteric sites in enzymes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Scoring residue conservation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Enzyme function less conserved than anticipated.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

THEMATICS: a simple computational predictor of enzyme function from structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Prediction of functionally important residues based solely on the computed energetics of protein structure.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Structure of the TPR domain of p67phox in complex with Rac.GTP

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Twilight zone of protein sequence alignments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

An evolutionary trace method defines binding surfaces common to protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

A hot spot of binding energy in a hormone-receptor interface

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Structure of phosphate-free ribonuclease A refined at 1.26 .ANG

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Control of enzyme activity by an engineered disulfide bond

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Information-theoretical entropy as a measure of sequence variability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

Human growth hormone and extracellular domain of its receptor: crystal structure of the complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2974822

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

6 July 2018

1 reference

Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation.

21 January 2018

1 reference

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.

21 January 2018

1 reference

Using a neural network and spatial clustering to predict the location of active sites in enzymes.

21 January 2018

1 reference

A method for localizing ligand binding pockets in protein structures.

21 January 2018

1 reference

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.

21 January 2018

1 reference

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification

21 January 2018

1 reference

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

21 January 2018

1 reference

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

21 January 2018

1 reference

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Automated discovery of 3D motifs for protein function annotation

21 January 2018

1 reference

Detection of functionally important regions in "hypothetical proteins" of known structure

21 January 2018

1 reference

Evolution of neural precursor selection: functional divergence of proneural proteins.

21 January 2018

1 reference

21 January 2018

1 reference

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

21 January 2018

1 reference

Automatic methods for predicting functionally important residues

21 January 2018

1 reference

12 December 2020

Intracellular Location and Cell Context-Dependent Function of Protein Kinase D

1 reference

12 December 2020

Small-world network approach to identify key residues in protein-protein interaction

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.406

1 reference

1 August 2017

1 reference

1 August 2017

1 reference