The Phyre2 web portal for protein modeling, prediction and analysis (Q29616136)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

title

The Phyre2 web portal for protein modeling, prediction and analysis (English)

2 references

PubMed

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

Christopher M Yates

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

7 March 2020

language of work or name

1 reference

30 April 2017

publication date

7 May 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

page(s)

845-858

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

Critical assessment of methods of protein structure prediction (CASP)--round x

7 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=5298202

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

3DLigandSite: predicting ligand-binding sites using similar structures

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

I-TASSER: a unified platform for automated protein structure and function prediction

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

A method and server for predicting damaging missense mutations

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Protein structure prediction on the Web: a case study using the Phyre server

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Protein homology detection by HMM-HMM comparison

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Protein secondary structure prediction based on position-specific scoring matrices

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

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

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

ePlant and the 3D data display initiative: integrative systems biology on the world wide web

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features

30 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Functional assignment of Mycobacterium tuberculosis proteome revealed by genome-scale fold-recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

CDD: conserved domains and protein 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=5298202

Improved model quality assessment using ProQ2.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Template-based protein structure modeling using the RaptorX web server.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

SIFT web server: predicting effects of amino acid substitutions on 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=5298202

Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

fpocket: online tools for protein ensemble pocket detection and tracking.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Protein folding requires crowd control in a simulated cell.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Structure prediction for CASP8 with all-atom refinement using Rosetta.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

PiSite: a database of protein interaction sites using multiple binding states in the PDB

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Fast procedure for reconstruction of full-atom protein models from reduced representations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Improving the accuracy of transmembrane protein topology prediction using evolutionary information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Residue-rotamer-reduction algorithm for the protein side-chain conformation problem.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

The structure of the protein universe and genome evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

MaxSub: an automated measure for the assessment of protein structure prediction quality.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

Predicting functionally important residues from sequence conservation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5298202

GAME: detecting cis-regulatory elements using a genetic algorithm

26 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNPROT.2015.053

31 March 2020

Identifiers

DOI

10.1038/NPROT.2015.053

3 references

PubMed

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

7 March 2020

1001304490

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

3 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25950237

7 March 2020

PubMed publication ID

3 references

30 April 2017

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25950237%20AND%20SRC:MED&resulttype=core&format=json