Protein threading using context-specific alignment potential (Q36960683)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23812991%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

title

Protein threading using context-specific alignment potential (English)

1 reference

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4 March 2020

2

1 reference

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4 March 2020

author name string

Jianzhu Ma

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23812991%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

Feng Zhao

series ordinal

3

1 reference

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4 March 2020

Jinbo Xu

series ordinal

4

1 reference

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4 March 2020

language of work or name

English

0 references

publication date

1 July 2013

1 reference

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4 March 2020

1 reference

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4 March 2020

volume

29

1 reference

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4 March 2020

issue

13

1 reference

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4 March 2020

page(s)

i257-65

1 reference

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Protein structure alignment beyond spatial proximity

4 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

A conditional neural fields model for protein threading

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Protein 8‐class secondary structure prediction using conditional neural fields

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Sequence context-specific profiles for homology searching

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Matt: local flexibility aids protein multiple structure alignment.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Statistical potential for assessment and prediction of protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

FFAS03: a server for profile--profile sequence alignments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Protein homology detection by HMM-HMM comparison

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

RAPTOR: optimal protein threading by linear programming

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

The PSIPRED protein structure prediction server

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Processing and analysis of CASP3 protein structure predictions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Profile hidden Markov models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Evaluation of comparative protein modeling by MODELLER

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Protein structure comparison by alignment of distance matrices

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

A new approach to protein fold recognition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Topology fingerprint approach to the inverse protein folding problem

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Amino acid substitution matrices from protein blocks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Sequence Alignment as Hypothesis Testing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Fast protein fold recognition via sequence to structure alignment and contact capacity potentials

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Incorporating homologues into sequence embeddings for protein analysis.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

Global optimum protein threading with gapped alignment and empirical pair score functions

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3694651

On the limited memory BFGS method for large scale optimization

4 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT210

Structure-derived substitution matrices for alignment of distantly related sequences

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23812991

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTT210

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23812991%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/MaWZX13

4 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23812991%20AND%20SRC:MED&resulttype=core&format=json

4 March 2020

PubMed publication ID

23812991

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23812991%20AND%20SRC:MED&resulttype=core&format=json