(Q34168536)

31 July 2017

Functionally important positions can comprise the majority of a protein's architecture (English)

1 reference

31 July 2017

Liskin Swint-Kruse

3

0 references

author name string

Sudheer Tungtur

series ordinal

1

1 reference

PubMed ID

21374721

31 July 2017

Daniel J Parente

series ordinal

2

1 reference

PubMed ID

21374721

31 July 2017

language of work or name

English

0 references

publication date

4 March 2011

1 reference

31 July 2017

1 reference

31 July 2017

79

1 reference

31 July 2017

5

1 reference

31 July 2017

1589-1608

1 reference

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Combining specificity determining and conserved residues improves functional site prediction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Coevolution in defining the functional specificity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

SNAP predicts effect of mutations on protein function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Subdividing repressor function: DNA binding affinity, selectivity, and allostery can be altered by amino acid substitution of nonconserved residues in a LacI/GalR homologue

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Analysis of the residue-residue coevolution network and the functionally important residues in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

An integrated system for studying residue coevolution in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Dendroscope: An interactive viewer for large phylogenetic trees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Identification of functional paralog shift mutations: conversion of Escherichia coli malate dehydrogenase to a lactate dehydrogenase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Clustal W and Clustal X version 2.0

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Extrinsic interactions dominate helical propensity in coupled binding and folding of the lactose repressor protein hinge helix

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Predicting specificity-determining residues in two large eukaryotic transcription factor families

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

MINER: software for phylogenetic motif identification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Predicting functional sites with an automated algorithm suitable for heterogeneous datasets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Predicting protein functional sites with phylogenetic motifs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

UCSF Chimera--a visualization system for exploratory research and analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

WebLogo: A Sequence Logo Generator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

MUSCLE: multiple sequence alignment with high accuracy and high throughput

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Evolutionarily conserved networks of residues mediate allosteric communication in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

A closer view of the conformation of the Lac repressor bound to operator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Effective use of sequence correlation and conservation in fold recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

The structure of PurR mutant L54M shows an alternative route to DNA kinking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

An evolutionary trace method defines binding surfaces common to protein families

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coli K12

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076786

Prediction of protein functional residues from sequence by probability density estimation.

5 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Improving position-specific predictions of protein functional sites using phylogenetic motifs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Phylogeny-independent detection of functional residues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Tracing evolutionary pressure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22985

Prediction of orthologous relationship by functionally important sites

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21374721

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22985

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

21374721