(Q37487949)

20 August 2017

Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures (English)

1 reference

20 August 2017

0 references

1 reference

Yi-Fei Huang

1

0 references

author name string

G Brian Golding

series ordinal

2

1 reference

20 August 2017

16 January 2014

1 reference

PLOS Computational Biology

20 August 2017

1 reference

20 August 2017

10

1 reference

20 August 2017

1

1 reference

20 August 2017

e1003429

1 reference

Creative Commons Attribution 4.0 International

20 August 2017

start time

16 January 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Bio++: efficient extensible libraries and tools for computational molecular evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Integrating sequence variation and protein structure to identify sites under selection

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Database resources of the National Center for Biotechnology Information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

PAML 4: phylogenetic analysis by maximum likelihood

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

ROCR: visualizing classifier performance in R

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

The B7 family of immune-regulatory ligands

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Different versions of the Dayhoff rate matrix

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Combining phylogenetic and hidden Markov models in biosequence analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Prediction of functional sites in proteins using conserved functional group analysis.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Protein evolution with dependence among codons due to tertiary structure.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Inference of functional regions in proteins by quantification of evolutionary constraints

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Crystal structure of the B7-1/CTLA-4 complex that inhibits human immune responses

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Structure and dimerization of a soluble form of B7-1

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

An evolutionary trace method defines binding surfaces common to protein families

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

A Hidden Markov Model approach to variation among sites in rate of evolution

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Both extracellular immunoglobin-like domains of CD80 contain residues critical for binding T cell surface receptors CTLA-4 and CD28

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Evolutionary trees from DNA sequences: A maximum likelihood approach

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

The rapid generation of mutation data matrices from protein sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

A space-time process model for the evolution of DNA sequences.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Assessing site-interdependent phylogenetic models of sequence evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Spatial distribution of selection pressure on a protein based on the hierarchical Bayesian model

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Estimating empirical codon hidden Markov models

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Detecting patches of protein sites of influenza A viruses under positive selection

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Solvent exposure imparts similar selective pressures across a range of yeast proteins.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

A nonparametric method for accommodating and testing across-site rate variation

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Predicting functionally important residues from sequence conservation.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Computing Bayes factors using thermodynamic integration.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

In silico identification of functional regions in proteins

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3894161

Equation of State Calculations by Fast Computing Machines

2 September 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003429

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003429

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003429

Tertiary Windowing to Detect Positive Diversifying Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003429

New Methods for Detecting Lineage-Specific Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003429

Inferring sequence regions under functional divergence in duplicate genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003429

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

21 January 2018

1 reference

12 December 2020

Three-dimensional window analysis for detecting positive selection at structural regions of proteins

1 reference

12 December 2020

Enzyme evolution explained (sort of)

1 reference

12 December 2020

Site interdependence attributed to tertiary structure in amino acid sequence evolution

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1003429

Identifiers

DOI

1 reference

20 August 2017

journals/ploscb/HuangG14

1 reference

DBLP Dataset 2021-01-02

release_kxoyt3lokzat3g7aui5w6ca7ai

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kxoyt3lokzat3g7aui5w6ca7ai

24 November 2022

mapped directly with Wikidata item

PMC publication ID

3894161

1 reference

PMC publication ID

3894161

20 August 2017

PubMed publication ID

24453956

1 reference

PMC publication ID

3894161