(Q30369735)

4 September 2017

SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model (English)

1 reference

4 September 2017

0 references

3

1 reference

4 September 2017

Wei Zhang

1

1 reference

4 September 2017

Song Liu

series ordinal

2

1 reference

4 September 2017

language of work or name

English

0 references

publication date

4 June 2008

1 reference

4 September 2017

1 reference

4 September 2017

3

1 reference

4 September 2017

6

1 reference

4 September 2017

e2325

1 reference

Creative Commons Attribution 4.0 International

4 September 2017

start time

4 June 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Real-value prediction of backbone torsion angles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Critical assessment of methods of protein structure prediction-Round VII

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Template-based modeling and free modeling by I-TASSER in CASP7.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Automated server predictions in CASP7

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Fams-ace: a combined method to select the best model after remodeling all server 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=2391293

Analysis of TASSER-based CASP7 protein structure prediction results.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Pcons.net: protein structure prediction meta 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=2391293

DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Support vector machines for prediction of dihedral angle regions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Sequence comparison and 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=2391293

A machine learning information retrieval approach to protein 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=2391293

On the origin and highly likely completeness of single-domain protein 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=2391293

Improved pairwise alignments of proteins in the Twilight Zone using local 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=2391293

Assessment of predictions submitted for the CASP6 comparative modeling category

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

The HHpred interactive server for protein homology detection and 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=2391293

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Combining prediction of secondary structure and solvent accessibility in 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=2391293

Local backbone structure prediction of 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=2391293

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Alignment of protein sequences by their profiles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

MUSCLE: multiple sequence alignment with high accuracy and high throughput

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Protein backbone angle prediction with machine learning approaches.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Automated prediction of CASP-5 structures using the Robetta 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=2391293

PROSPECT II: protein structure prediction program for genome-scale applications.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

Protein threading by linear programming

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

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=2391293

Bayesian probabilistic approach for predicting backbone structures in terms of 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=2391293

HMMSTR: a hidden Markov model for local sequence-structure correlations in 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=2391293

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=2391293

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=2391293

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

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=2391293

The FSSP database of structurally aligned protein fold families

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

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=2391293

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=2391293

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2391293

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=2391293

The nature of the accessible and buried surfaces in 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=2391293

The PDB is a covering set of small protein structures

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

SPARKS 2 and SP3 servers in CASP6.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Identification of related proteins on family, superfamily and fold level.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Variable gap penalty for protein sequence-structure alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Protein Structural Motif Prediction in Multidimensional ø-ψ Space Leads to Improved Secondary Structure Prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Fold recognition by concurrent use of solvent accessibility and residue depth

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0002325

Alignment of the amino acid sequences of distantly related proteins using variable gap penalties

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18523556

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Estimation and use of protein backbone angle probabilities

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18523556

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0002325

1 reference

4 September 2017

0 references

1 reference

4 September 2017

PubMed publication ID

18523556

1 reference