(Q35133200)

6 August 2017

title

MRFalign: protein homology detection through alignment of Markov random fields (English)

1 reference

6 August 2017

2

0 references

author name string

Jianzhu Ma

series ordinal

1

1 reference

6 August 2017

Zhiyong Wang

series ordinal

3

1 reference

6 August 2017

Jinbo Xu

series ordinal

4

1 reference

6 August 2017

publication date

27 March 2014

1 reference

PLOS Computational Biology

6 August 2017

published in

1 reference

6 August 2017

volume

10

1 reference

6 August 2017

issue

3

1 reference

6 August 2017

page(s)

e1003500

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Creative Commons Attribution 4.0 International

6 August 2017

copyright license

start time

27 March 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Predicting protein contact map using evolutionary and physical constraints by integer programming

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Protein threading using context-specific alignment potential

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Protein structure alignment beyond spatial proximity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

A large-scale evaluation of computational protein function prediction

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Discriminative modelling of context-specific amino acid substitution probabilities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

A conditional neural fields model for protein threading

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

A position-specific distance-dependent statistical potential for protein structure and functional study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Accelerated Profile HMM Searches

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Protein molecular function prediction by Bayesian phylogenomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

TM-align: a protein structure alignment algorithm based on the TM-score

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Protein homology detection by HMM-HMM comparison

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

SWISS-MODEL: An automated protein homology-modeling server

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Profile-profile alignment: a powerful tool for protein structure prediction.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Using the Fisher kernel method to detect remote protein homologies.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Comparison of sequence profiles. Strategies for structural predictions using sequence information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

The ASTRAL compendium for protein structure and sequence analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Hidden Markov models for detecting remote protein homologies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Intermediate sequences increase the detection of homology between sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Searching databases of conserved sequence regions by aligning protein multiple-alignments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

SCOP: a structural classification of proteins database for the investigation of sequences and structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Progressive sequence alignment as a prerequisite to correct phylogenetic trees

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

PROSITE: a dictionary of sites and patterns in proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Multiple sequence alignment based on profile alignment of intermediate sequences.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Matt: local flexibility aids protein multiple structure alignment.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Mismatch string kernels for discriminative protein classification

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

The spectrum kernel: a string kernel for SVM protein classification.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3967925

Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003500

Multi-view prediction of protein function

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003500

SATCHMO: sequence alignment and tree construction using hidden Markov models

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24675572

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24675572

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003500

1 reference

6 August 2017

1 reference

journals/ploscb/MaWWX14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

6 August 2017

1 reference