OCTOPUS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool OCTOPUS
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Tool usage distribution map

This map represents all the scientific publications referring to OCTOPUS per scientific context
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Associated diseases

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Protocols

OCTOPUS specifications

Information


Unique identifier OMICS_14317
Name OCTOPUS
Alternative name obtainer of correct topologies for uncharacterized sequences
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Output data A predicted transmembrane protein topology.
Output format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Arne Elofsson

Information


Unique identifier OMICS_14317
Name OCTOPUS
Alternative name obtainer of correct topologies for uncharacterized sequences
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data An amino acid sequence.
Input format FASTA
Output data A predicted transmembrane protein topology.
Output format FASTA
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
CMake, GCC, Perl, BLAST, PSI-BLAST
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Arne Elofsson

Publication for obtainer of correct topologies for uncharacterized sequences

OCTOPUS citations

 (38)
library_books

Cross species analysis of apical asparagine rich protein of Plasmodium vivax and Plasmodium knowlesi

2018
Sci Rep
PMCID: 5893618
PMID: 29636493
DOI: 10.1038/s41598-018-23728-1

[…] ively. No transmembrane region and GPI-anchor motif were predicted for PvAARP and PkAARP or PfAARP, according to several robust transmembrane prediction algorithms such as TMHMM ver 2.0, Phobius, and OCTOPUS–, despite a previous report of a predicted transmembrane domain in PfAARP. Thus, we inferred that AARP proteins probably do not possess a transmembrane domain. The apical Asn-rich region in Pv […]

call_split

Statistically derived asymmetric membrane potentials from α helical and β barrel membrane proteins

2018
Sci Rep
PMCID: 5849751
PMID: 29535329
DOI: 10.1038/s41598-018-22476-6
call_split See protocol

[…] ies of our potentials are somewhat higher. The asymmetric Ez potential of Schramm & DeGrado on lipid-accessible residues yields an accuracy of 72.8%, while the sequence-based state-of-the-art methods OCTOPUS and the meta-server TopCons (both of which contain a machine learning component) predicts OPM topologies for 72.1% and 74.8% of the protein chains. For β-barrel proteins, our potentials predic […]

library_books

AtOMA1 Affects the OXPHOS System and Plant Growth in Contrast to Other Newly Identified ATP Independent Proteases in Arabidopsis Mitochondria

2017
Front Plant Sci
PMCID: 5594102
PMID: 28936218
DOI: 10.3389/fpls.2017.01543

[…] risingly, we found that the AtOCT1 protease is an integral membrane protein, in contrast with the matrix localization of yeast and human homologs. This last finding is supported by analysis using the OCTOPUS software (), which predicts a hydrophobic region within the C-terminal end of AtOCT1 sequence. This region is not present in the yeast and mammalian counterparts (Supplementary Table ).The Ara […]

library_books

A membrane inserted structural model of the yeast mitofusin Fzo1

2017
Sci Rep
PMCID: 5578988
PMID: 28860650
DOI: 10.1038/s41598-017-10687-2

[…] ary Fig. ). For this reason, the ab initio prediction of the helix dimer structure was crucial in the modelling process.The location of the TM segments was identified using the predictors MEMSAT-SVM, OCTOPUS and TMpred (Supplementary Table ). Ab initio modelling of the TM segments was performed using the PREDDIMER server, and the best model was selected according to the proposed ranking score (F S […]

library_books

Prostaglandin E2 glyceryl ester is an endogenous agonist of the nucleotide receptor P2Y6

2017
Sci Rep
PMCID: 5443783
PMID: 28539604
DOI: 10.1038/s41598-017-02414-8

[…] model to achieve energetically favorable hybrid template models. Any residues still lacking coordinates were modeled de novo using 3mer and 9mer fragments. Transmembrane segments, as predicted using OCTOPUS, were modeled within Rosetta’s implicit membrane potential. In total, 32,000 all-atom models were generated. The resulting full sequence models were subjected to eight iterative cycles of side […]

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

[…] karyotes is presented in . It is clear that some of the advanced methods perform better than others. Those achieving the highest sensitivity and precision are PredαTM , , TOPCONS , HMMTOP , Philius , OCTOPUS , SCAMPI and SVMtop . The PredαTM predictor [,91] is independent of any explicitly expressed evolution information, thus has an added advantage over the aforementioned algorithms when predict […]


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OCTOPUS institution(s)
Department of Biochemistry and Biophysics/Center for Biomembrane Research/Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
OCTOPUS funding source(s)
This work was supported by grants from the Swedish Natural Sciences Research Council, the Wallenberg Consortium North, the Knut & Alice Wallenberg Foundation and the Foundation for Strategic Research.

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