TOPCONS statistics

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Citations per year

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

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

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Popular tool citations

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Protocols

TOPCONS specifications

Information


Unique identifier OMICS_07262
Name TOPCONS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Operating system Unix/Linux
Programming languages C, Java, Perl
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Arne Elofsson

Additional information


https://github.com/ElofssonLab/TOPCONS2/

Information


Unique identifier OMICS_07262
Name TOPCONS
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Arne Elofsson

Additional information


https://github.com/ElofssonLab/TOPCONS2/

Publications for TOPCONS

TOPCONS citations

 (164)
call_split

The LetA/S two component system regulates transcriptomic changes that are essential for the culturability of Legionella pneumophila in water

2018
Sci Rep
PMCID: 5928044
PMID: 29712912
DOI: 10.1038/s41598-018-24263-9
call_split See protocol

[…] ing within LetS. The Accession number YP_095929.1 representing Lpg1912 of Legionella pneumophila Philadelphia-1 strain was queried. The TMHMM server v. 2.0 (http://www.cbs.dtu.dk/services/TMHMM/) and TOPCONS (http://topcons.net/) were used to predict the transmembrane helices on the N-terminal of LetS,. […]

library_books

Evidence for functional pre coupled complexes of receptor heteromers and adenylyl cyclase

2018
Nat Commun
PMCID: 5871782
PMID: 29593213
DOI: 10.1038/s41467-018-03522-3

[…] the same six TMs for the M2 domain (TM 7 to TM 12), but there was discrepancy on the predicted TMs of the M1 domain. Taking into account the orientation of the predicted TM helices, only Uniprot and TOPCONS solutions were compatible with the well-established intracellular N-terminal and C-terminal domains of AC5. First, TM peptides mimicking right-oriented TMs derived from Uniprot predictions (ab […]

library_books

Molecular Characterization of a Dual Domain Carbonic Anhydrase From the Ctenidium of the Giant Clam, Tridacna squamosa, and Its Expression Levels After Light Exposure, Cellular Localization, and Possible Role in the Uptake of Exogenous Inorganic Carbon

2018
Front Physiol
PMCID: 5879104
PMID: 29632495
DOI: 10.3389/fphys.2018.00281

[…] CAs (CA4/CA9/CA15; Table ) while the second α-CA domain (residue 315–564) display high similarity with CA4 (Table ). There was a ~53% sequence similarity between these two α-CA domains. Based on the TOPCONS program (http://topcons.net/; Tsirigos et al., ), the DDCA of T. squamosa probably consisted of two TMs. The first TM (residue 156–176) was located inside the first CA domain while the second […]

library_books

Crystal structure of undecaprenyl pyrophosphate phosphatase and its role in peptidoglycan biosynthesis

2018
Nat Commun
PMCID: 5852022
PMID: 29540682
DOI: 10.1038/s41467-018-03477-5

[…] deller was used to model the invert-state based on this sequence alignment. The topological orientation of BacA within the bacterial cytoplasmic membrane was predicted using sequence-based approaches TOPCONS and MEMSAT-SVM and the structure-based method Memembed.GROMACS v5.1.2 was used to perform all molecular dynamics simulations (MDS). Coarse grained (CG) MDS with the Martini 2.2 force field, we […]

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

[…] mewhat 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 predict OPM topologies for 91.7% o […]

library_books

Characterization and Comparative Analysis of Olfactory Receptor Co Receptor Orco Orthologs Among Five Mirid Bug Species

2018
Front Physiol
PMCID: 5845112
PMID: 29556202
DOI: 10.3389/fphys.2018.00158

[…] firmed with LA Taq DNA polymerase (Takara, Dalian, China) by PCR using gene-specific primers (Table ).The full length Orco sequences were aligned by ClustalX 2.1 and edited by GeneDoc 2.7.0 software. TOPCONS (http://topcons.cbr.su.se/) (Tsirigos et al., ) was used to identify the number and location of predicted transmembrane domains. The topology diagrams were constructed using TOPO2 Transmembran […]


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TOPCONS institution(s)
Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Solna, Sweden; Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm University, Sweden
TOPCONS funding source(s)
Supported by the Swedish Research Council [VR-NT 2012–5046, VR-M 2010–3555]; Foundation for Strategic Research; Swedish Escience Research Center and BILS (Bioinformatics Infrastructure for Life Science).

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