(Q30353463)

21 August 2017

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. (English)

1 reference

protein structure prediction

21 August 2017

0 references

0 references

1 reference

Jianyi Yang

3

0 references

author name string

Renxiang Yan

1

1 reference

21 August 2017

Dong Xu

2

1 reference

21 August 2017

Sara Walker

4

1 reference

21 August 2017

Yang Zhang

5

1 reference

21 August 2017

language of work or name

English

0 references

publication date

1 January 2013

1 reference

21 August 2017

1 reference

21 August 2017

3

1 reference

21 August 2017

2619

1 reference

Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported

21 August 2017

start time

10 September 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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3 June 2018

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3 June 2018

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3 June 2018

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3 June 2018

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Progress and challenges in protein structure prediction

3 June 2018

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3 June 2018

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Automated server predictions in CASP7

3 June 2018

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A comprehensive system for evaluation of remote sequence similarity detection

3 June 2018

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LOMETS: a local meta-threading-server for protein structure prediction

3 June 2018

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Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology

3 June 2018

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FFAS03: a server for profile--profile sequence alignments

3 June 2018

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Prediction of solvent accessibility and sites of deleterious mutations from protein sequence.

3 June 2018

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

3 June 2018

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The protein structure prediction problem could be solved using the current PDB library

3 June 2018

1 reference

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LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction.

3 June 2018

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Protein homology detection by HMM-HMM comparison

3 June 2018

1 reference

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Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

3 June 2018

1 reference

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Scoring function for automated assessment of protein structure template quality

3 June 2018

1 reference

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Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Scoring profile-to-profile sequence alignments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Automated structure prediction of weakly homologous proteins on a genomic scale

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

A comparison of scoring functions for protein sequence profile alignment.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

3D-Jury: a simple approach to improve protein structure predictions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

A comparison of profile hidden Markov model procedures for remote homology detection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Protein structure prediction and structural genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

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

3 June 2018

1 reference

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3 June 2018

The Protein Data Bank

1 reference

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Protein secondary structure prediction based on position-specific scoring matrices

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Hidden Markov models for detecting remote protein homologies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Profile hidden Markov models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Comparative protein modelling by satisfaction of spatial restraints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Hidden Markov models in computational biology. Applications to protein modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Identification of common molecular subsequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

A general method applicable to the search for similarities in the amino acid sequence of two proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Profile analysis: detection of distantly related proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Rapid and sensitive protein similarity searches

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Basic local alignment search tool

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Amino acid substitution matrices from protein blocks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition.

3 June 2018

1 reference

Critical assessment of methods of protein structure prediction - Round VIII.

21 January 2018

1 reference

CAFASP3: The third critical assessment of fully automated structure prediction methods

21 January 2018

1 reference

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

21 January 2018

1 reference

A study on protein sequence alignment quality

21 January 2018

1 reference

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

21 January 2018

1 reference

Protein threading using PROSPECT: design and evaluation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3965362

Position-based sequence weights

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24018415

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

SABmark--a benchmark for sequence alignment that covers the entire known fold space

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24018415

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/SREP02619

1 reference

Dimensions Publication ID

21 August 2017

1047171773

0 references

Fatcat ID

release_xhwt4vrd5fba3gazs3dth2fbge

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/xhwt4vrd5fba3gazs3dth2fbge

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

21 August 2017

1 reference