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MPtopo specifications

Information


Unique identifier OMICS_23465
Name MPtopo
Restrictions to use None
Community driven No
Data access Browse, Application programming interface
User data submission Not allowed
Maintained Yes

Maintainer


Publication for MPtopo

MPtopo citations

 (7)
library_books

Quantitative Residue Level Structure–Evolution Relationships in the Yeast Membrane Proteome

2013
Genome Biol Evol
PMCID: 3641637
PMID: 23512408
DOI: 10.1093/gbe/evt039

[…] ” in the Saccharomyces Genome Database () and 2) the set of membrane proteins of known 3D structure from the Protein Data Bank () that are divided into TM and EM regions based on annotations from the MPtopo database (). We then identified the most significant sequence alignment between each yeast ORF and a membrane protein of known 3D structure based on alignment E value, as determined using the g […]

library_books

TOPPER: Topology Prediction of Transmembrane Protein Based on Evidential Reasoning

2013
Sci World J
PMCID: 3562663
PMID: 23401665
DOI: 10.1155/2013/123731

[…] In this paper, a data set of 125 transmembrane protein sequences with known topology is collected from the data set of MPtopo [] to verify the effectiveness of the proposed method TOPPER.In order to reflect the performance of combination predictor faithfully and to avoid overfitting, the experiment is performed using […]

library_books

A Simple Method for Predicting Transmembrane Proteins Based on Wavelet Transform

2012
PMCID: 3535531
PMID: 23289014
DOI: 10.7150/ijbs.5371

[…] k that choosing FP hydrophobic parameters is the best to only predict TMHs. While KD hydrophobic parameters is the best when combined with the prediction accuracy of residues.We pick PDB ID 1KQG from MPtopo database as an example and choose KD hydrophobic parameters to describe this method to predict the number and position of membrane protein TMHs. Also we predict 13 groups of membrane protein se […]

library_books

A Folding Pathway Dependent Score to Recognize Membrane Proteins

2011
PLoS One
PMCID: 3046963
PMID: 21390303
DOI: 10.1371/journal.pone.0016778

[…] A dataset increases (). We conclude that in mitochondria, the process of membrane localization may not be similar to the four-step membrane protein folding process ().We take another dataset from the MPtopo database (). Based on whether the protein helix bundles are determined from three dimensional structure or by biochemical experimental methods, Jayasinghe et al. have divided the MPtopo databas […]

library_books

ProDaMa: an open source Python library to generate protein structure datasets

2009
BMC Res Notes
PMCID: 2761932
PMID: 19799773
DOI: 10.1186/1756-0500-2-202

[…] ii) information about protein structure classification from CATH [] and SCOP [], iii) other protein data from the PDBFINDER database [], and iv) information about membrane protein topologies from the MPTopo database []. […]

library_books

IgTM: An algorithm to predict transmembrane domains and topology in proteins

2008
BMC Bioinformatics
PMCID: 2566583
PMID: 18783592
DOI: 10.1186/1471-2105-9-367

[…] gous proteins, extracted form SwissProt database, used in [,]. These proteins were selected from a set of 155 proteins, discarding those with more than 25% of similarity.The last dataset used was the MPTOPO dataset []. In its last version (August 2007) the set contains 185 proteins: 25 of them β-barrels and the rest α-helix transmembrane. All the segments have been experimentally validated. The 3D […]

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MPtopo institution(s)
Department of Physiology and Biophysics and the Program in Structural Biology, University of California, Irvine, CA, USA
MPtopo funding source(s)
Supported by National Institutes of General Medical Sciences (GM-46823).

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