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Protocols

MP-T specifications

Information


Unique identifier OMICS_17625
Name MP-T
Alternative name Membrane Protein Threader
Interface Web user interface
Restrictions to use None
Input data An IMembrane structure data, a sequence protein data.
Input format TEM, FASTA
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Charlotte Deane

Publication for Membrane Protein Threader

MP-T citations

 (3)
library_books

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

2017
Comput Struct Biotechnol J
PMCID: 5312651
PMID: 28228927
DOI: 10.1016/j.csbj.2017.01.008

[…] er. To date, the tertiary structure prediction of membrane proteins remains a significant challenge, but the recent development of methods specifically optimized to align membrane proteins (AlignMe , MP-T , PRALINE™ , TM-Coffee ) enable promising progress. Significant advances have been made in the last decade on methods for predicting helix–helix interactions, but the methods for the optimal pack […]

call_split

A voltage dependent fluorescent indicator for optogenetic applications, archaerhodopsin 3: Structure and optical properties from in silico modeling

2017
F1000Res
PMCID: 5381632
PMID: 28435665
DOI: 10.5256/f1000research.11514.r19223
call_split See protocol

[…] n, we tested three algorithms of pairwise alignment using their results as an input for each method of model building. Two of the alignment methods are specifically constructed for membrane proteins, MP-T and AlignMe , and the third one, MUSTER , gains its quality from evolutionary predictions. The latter algorithm is a built-in algorithm of I-TASSER suite and its results were used only for this […]

library_books

Comprehensive, structurally informed alignment and phylogeny of vertebrate biogenic amine receptors

2015
PeerJ
PMCID: 4338800
PMID: 25737813
DOI: 10.7717/peerj.773

[…] porate structural information into the alignment algorithm by aligning sequences to a given protein crystal structure (; ) or hidden Markov model (HMM) profile (; ; ). In fact, some programs, such as MP-T () and TM-Coffee (), cater specifically to membrane proteins. However, all of these programs are extremely computationally-intensive and thus ill-suited for large-scale applications. Furthermore, […]

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MP-T institution(s)
Department of Statistics, University of Oxford, Oxford, UK
MP-T funding source(s)
This work was supported by the Engineering and Physical Sciences Research Council, the Biological Sciences Research Council and the University of Oxford Doctoral Training Centres.

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