SPOCTOPUS statistics

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Citations per year

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

This map represents all the scientific publications referring to SPOCTOPUS per scientific context
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Protocols

SPOCTOPUS specifications

Information


Unique identifier OMICS_03896
Name SPOCTOPUS
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SPOCTOPUS

SPOCTOPUS citations

 (21)
library_books

A Novel Modeling in Mathematical Biology for Classification of Signal Peptides

2018
Sci Rep
PMCID: 5773712
PMID: 29348418
DOI: 10.1038/s41598-018-19491-y

[…] Amino Acid Composition. Multiple classifications of protein are offered in. The perception of difference between signal sequence and its peptide chain is manipulated by predictors SS- and SP-indexes. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology based on neural networks, hidden Markov model (HMM) and dynamic programming algorithm is proposed in. Various researche […]

library_books

Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment*

2017
PMCID: 5795391
PMID: 29141914
DOI: 10.1074/mcp.RA117.000400

[…] d supplemental Fig. S2A) was compiled by calculating the intersections of four data sets: “Predicted secreted proteins,” “SignalP predicted secreted proteins,” “Phobius predicted secreted proteins,” “SPOCTOPUS predicted secreted proteins” downloaded from the Human Protein Atlas:http://www.proteinatlas.org/search/protein_class:Predicted%20secreted%20proteinshttp://www.proteinatlas.org/search/protei […]

library_books

The bacterial Sec system is required for the organization and function of the MreB cytoskeleton

2017
PLoS Genet
PMCID: 5629013
PMID: 28945742
DOI: 10.1371/journal.pgen.1007017

[…] and EnvC, which were shown to be inserted into the membrane and transported to the periplasm by the Sec system, respectively [,] and FtsK, which contains a potential signal sequence (as predicted by SPOCTOPUS []). However, our results point at MreB, which has been shown to be recruited to the forming septum in E. coli by FtsZ during the initial stages of cell division to enable Z-ring constrictio […]

library_books

Syp1 regulates the clathrin mediated and clathrin independent endocytosis of multiple cargo proteins through a novel sorting motif

2017
Mol Biol Cell
PMCID: 5576906
PMID: 28701344
DOI: 10.1091/mbc.E15-10-0731

[…] annel.For cases in which protein topology is undetermined, motifs within Syp1 cargoes were assessed for residence in cytoplasmic regions of the protein using the membrane topology prediction software SPOCTOPUS (; http://octopus.cbr.su.se/). […]

call_split

Positive Allosteric Modulation of Insect Olfactory Receptor Function by ORco Agonists

2016
PMCID: 5145856
PMID: 28018173
DOI: 10.3389/fncel.2016.00275
call_split See protocol

[…] . Predicted TM topologies for OR53 (TOPCONS) were 33–53, 68–83, 123–143, 174–194, 252–272, 281–301, 354–374. For OR9, six TM regions were predicted with most TOPCONS sub-methods used. The OCTOPUS and SPOCTOPUS sub-methods, however, predicted seven TM domains at 56–76, 87–107, 148–168, 192–222, 288–308, 319–339, 389–409 with the last one being predicted only by these two algorithms. […]

library_books

The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains

2016
PLoS One
PMCID: 5104382
PMID: 27832149
DOI: 10.1371/journal.pone.0166274

[…] i.de/index.html; cleavage at T61), Signal BLAST (http://sigpep.services.came.sbg.ac.at/signalblast.html; cleavage at G58), Signal-CF (http://www.csbio.sjtu.edu.cn/bioinf/Signal-CF/; cleavage at A59), Spoctopus (http://octopus.cbr.su.se/; cleavage at G58), SPEPLip (http://gpcr.biocomp.unibo.it/cgi/predictors/spep/pred_spepcgi.cgi; cleavage at A59), Signal3L (http://www.csbio.sjtu.edu.cn/bioinf/Sign […]


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SPOCTOPUS institution(s)
Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm, Sweden; Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden

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