Transmembrane protein alignment and fold recognition based on predicted topology (Q30352431)

9 October 2017

Transmembrane protein alignment and fold recognition based on predicted topology (English)

1 reference

9 October 2017

transmembrane protein

0 references

0 references

Chao Zhang

3

0 references

author name string

Han Wang

1

1 reference

9 October 2017

Zhiquan He

2

1 reference

9 October 2017

Li Zhang

4

1 reference

9 October 2017

Dong Xu

5

1 reference

9 October 2017

language of work or name

English

0 references

publication date

19 July 2013

1 reference

9 October 2017

1 reference

9 October 2017

8

1 reference

9 October 2017

7

1 reference

9 October 2017

e69744

1 reference

Creative Commons Attribution 4.0 International

9 October 2017

start time

19 July 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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Ab initio modeling of small proteins by iterative TASSER simulations

3 June 2018

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Gene duplication of the eight-stranded beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane beta-barrels

3 June 2018

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transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels

3 June 2018

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Predicting the solvent accessibility of transmembrane residues from protein sequence

3 June 2018

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

3 June 2018

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A machine learning information retrieval approach to protein fold recognition.

3 June 2018

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Structure modeling of all identified G protein-coupled receptors in the human genome

3 June 2018

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The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology

3 June 2018

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3 June 2018

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3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme

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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3 June 2018

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Combining prediction of secondary structure and solvent accessibility in proteins

3 June 2018

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3 June 2018

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Protein homology detection by HMM-HMM comparison

3 June 2018

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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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Folding and assembly of beta-barrel membrane proteins

3 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3716705

3 June 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0069744

Scoring function for automated assessment of protein structure template quality

21 January 2018

1 reference

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PREDICT modeling and in-silico screening for G-protein coupled receptors.

3 June 2018

1 reference

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G protein-coupled receptors: in silico drug discovery in 3D.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3716705

PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane 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=3716705

Transmembrane proteins in the Protein Data Bank: identification and classification.

3 June 2018

1 reference

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A combined transmembrane topology and signal peptide prediction method

3 June 2018

1 reference

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Membrane channel structure of Helicobacter pylori vacuolating toxin: role of multiple GXXXG motifs in cylindrical channels.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3716705

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin.

3 June 2018

1 reference

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The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.

3 June 2018

1 reference

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

3 June 2018

1 reference

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Architecture of succinate dehydrogenase and reactive oxygen species generation

3 June 2018

1 reference

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TMPDB: a database of experimentally-characterized transmembrane topologies

3 June 2018

1 reference

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Reliability of transmembrane predictions in whole-genome data

3 June 2018

1 reference

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Asymmetric conductivity of engineered porins

3 June 2018

1 reference

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Transmembrane helix predictions revisited

3 June 2018

1 reference

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Drug design strategies for targeting G-protein-coupled receptors

3 June 2018

1 reference

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Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site

3 June 2018

1 reference

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Improved detection of homologous membrane proteins by inclusion of information from topology predictions.

3 June 2018

1 reference

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CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4.

3 June 2018

1 reference

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Processing and evaluation of predictions in CASP4

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3716705

The HMMTOP transmembrane topology prediction server

3 June 2018

1 reference

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MPtopo: A database of membrane protein topology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3716705

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

3 June 2018

1 reference

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The Protein Data Bank and the challenge of structural genomics

3 June 2018

1 reference

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A systematic approach to dynamic programming in bioinformatics

3 June 2018

1 reference

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Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 A resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3716705

The PSIPRED protein structure prediction server

3 June 2018

1 reference

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Processing and analysis of CASP3 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=3716705

SOSUI: classification and secondary structure prediction system for membrane proteins

3 June 2018

1 reference

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

3 June 2018

1 reference

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The structural alignment between two proteins: is there a unique answer?

3 June 2018

1 reference

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TopPred II: an improved software for membrane protein structure predictions

3 June 2018

1 reference

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Real value prediction of solvent accessibility from amino acid sequence.

3 June 2018

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MP-T: improving membrane protein alignment for structure prediction

21 January 2018

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Modeling ensembles of transmembrane beta-barrel proteins.

21 January 2018

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TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

21 January 2018

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An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes.

21 January 2018

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Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method

21 January 2018

1 reference

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Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

21 January 2018

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Reliability measures for membrane protein topology prediction algorithms.

21 January 2018

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TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins

21 January 2018

1 reference

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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.0069744

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=3716705

Improving transmembrane protein consensus topology prediction using inter-helical interaction

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23894534

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23894534

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Refining neural network predictions for helical transmembrane proteins by dynamic programming

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23894534

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0069744

1 reference

9 October 2017

0 references

1 reference

9 October 2017

1 reference