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TopPred specifications

Information


Unique identifier OMICS_07268
Name TopPred
Alternative name TOP-PRED
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Pascal
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.10
Stability No
Maintained No

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Publications for TopPred

TopPred citations

 (151)
library_books

JMJD8 is a novel endoplasmic reticulum protein with a JmjC domain

2017
Sci Rep
PMCID: 5684140
PMID: 29133832
DOI: 10.1038/s41598-017-15676-z

[…] The protein sequence of JMJD8 was obtained from NCBI (NM_001005920.2) and subjected to signal peptide analysis (Signal P 4.1), transmembrane motif analysis (TopPred2) and GlycoMine. The sequences of JmjC protein were retrieved from UniProtKB with the following accession numbers and amino acid regions: JHDM1A (Q9Y2K7; 148–316), JHDM1B (Q8NHM5; 178–346), JM […]

library_books

Cell surface Thomsen Friedenreich proteome profiling of metastatic prostate cancer cells reveals potential link with cancer stem cell like phenotype

2017
Oncotarget
PMCID: 5716753
PMID: 29228713
DOI: 10.18632/oncotarget.21985

[…] The consensus transmembrane topology prediction strategy was adopted and three transmembrane prediction software tools including TMHMM 2.0 (http://www.cbs.dtu.dk/services/TMHMM-2.0/), MPEx 3.2 and TopPred 0.01 (http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::toppred) were used to identify the transmembrane proteins (see for detail). […]

call_split

The single cyclic nucleotide specific phosphodiesterase of the intestinal parasite Giardia lamblia represents a potential drug target

2017
PLoS Negl Trop Dis
PMCID: 5617230
PMID: 28915270
DOI: 10.1371/journal.pntd.0005891
call_split See protocol

[…] were predicted using the programs TOPCONS 2.0 [] (metasearch with five programs), PSIPRED [] (MEMSAT-SVM and MEMSAT3 algorithms), Phobius/PolyPhobius [], TMHMM 2.0 [], TMSEG, PHDhtm [], TMPred [] and TopPred [], and a consensus was deduced from all predictions. Secondary structure predictions were done using iTasser, PSSpred and the “Predict Protein” web services [,]. […]

library_books

Structure, Expression, and Functional Analysis of the Hexokinase Gene Family in Cassava

2017
Int J Mol Sci
PMCID: 5454953
PMID: 28498327
DOI: 10.3390/ijms18051041

[…] rminal regions was performed using the subcellular prediction localization program TargetP 1.1 (http://www.cbs.dtu.dk/services/TargetP/) and prediction of the membrane anchored segment was done using TopPred2 (http://www.sbc.su.se/~erikw/toppred2/) []. For the phylogenetic analysis, HXKs from P. patens, A. thaliana, O. sativa, N. tabacum, R. communis, S. lycopersicum, and P. trichocarpa were align […]

library_books

New Insights on Leucine Rich Repeats Receptor Like Kinase Orthologous Relationships in Angiosperms

2017
Front Plant Sci
PMCID: 5380761
PMID: 28424707
DOI: 10.3389/fpls.2017.00381

[…] and KDs (PF00069.16)) are outputs of the hmmsearch program (default parameters) (). Island domains were determined based on predicted LRR positions in sequences. For SP and TM domains, the TMHMM and TOPPRED softwares have been used (; ). For the malectin domains in SG_I and SG_VIII-2, sequences of the domains were extracted in SMART and aligned to build hmm motifs with the hmmbuild program (; ). […]

call_split

A UPF0118 family protein with uncharacterized function from the moderate halophile Halobacillus andaensis represents a novel class of Na+(Li+)/H+ antiporter

2017
Sci Rep
PMCID: 5379678
PMID: 28374790
DOI: 10.1038/srep45936
call_split See protocol

[…] s performed using the website http://www.fruitfly.org/seq_tools/promoter.html. Transmembrane segment prediction was carried out by using the website http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::toppred . […]

Citations

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TopPred institution(s)
Ecole Normale Superieure, Laboratoire de Genetique Moleculaire, CNRS URA 1302, Paris, France; Karolinska Institute Center for Structural Biochemistry, NOVUM, Huddinge, Sweden
TopPred funding source(s)
Supported by grants from the Swedish Medical Research Council and the Axelsson-Johnsson Foundation.

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