ConPred protocols

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ConPred specifications

Information


Unique identifier OMICS_07258
Name ConPred
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability No
Maintained No

Publications for ConPred

ConPred in pipeline

2009
PMCID: 3032949
PMID: 21637656
DOI: 10.1590/S1415-47572009005000003

[…] set at zero to return the location of all aataaa and attaaa consensus signals, along with an associated score between 0 and 1. signal peptide search (signalp 3.0) and transmembrane prediction (conpred ii) of the deduced proteins were performed online., the level of dna identity between the kozak's consensus sequence (gccgccrccatgg, r = a/g) () and the flanking 13-nucleotides around […]

ConPred in publications

 (17)
PMCID: 5172438
PMID: 15629037
DOI: 10.1016/S1672-0229(04)02001-7

[…] of the original algorithm locating tm segments in queries is preserved (sensitivity of ~95% among documented proteins with helical tm regions). in 2003, xia and colleagues presented a new approach, conpred_elite , that can predict the whole topology with accuracies of 98% for prokaryotic and 95% for eukaryotic proteins as they reported., besides the tm helix, another tm segments type […]

PMCID: 5173181
PMID: 16689694
DOI: 10.1016/S1672-0229(05)03035-4

[…] of the full-length sequences of gpcrs with that only based on the intracellular part as adopted by other researches, we predicted the transmembrane helices of these gpcrs with the programs conpred ii and hmmtop 2.0 , then extracted the intracellular sequences and converted them into fixed-length feature vectors with the same method. the prediction results with k = 2 and k = 3 […]

PMCID: 4966943
PMID: 27472482
DOI: 10.1371/journal.pone.0159861

[…] for all procedures involving animals., recombinant gt2 (rgt2) was produced as the large extracellular domain (animo acids 23–247) from methanobrevibacter ruminantium m1 (mru_2175) predicted using conpred ii. the dna coding for the extracellular domain was synthesized (geneart; life technologies, usa) using escherichia coli codon preference and subcloned into pet-32a (novagen, usa) to create […]

PMCID: 4209838
PMID: 25371825
DOI: 10.1155/2014/129849

[…] the topology of oatp1b1 was predicted using the online prediction programs topcons [], phobius [], tmpred [], toppred ii [], membrain [], phdhtm [], split 4.0 [], philius [], hmmtop [], svmtm [], conpred ii [], sosui [], tmhmm [], tseg [], pred-tmr [], and memsat3 []. a homology model was generated using the protein homology/analogy recognition engine v 2.0 (phyre2) [], which modeled […]

PMCID: 3664084
PMID: 23679152
DOI: 10.1186/1471-2180-13-108

[…] sensitive database searching using hidden markov models (hmm) was performed using the program hmmer (http://hmmer.janelia.org/) []., all obtained predicted proteins were analyzed with the tmhmm, conpred ii and hmmtop algorithms [-] to test for the typical 7-transmembrane domain topology. for those few proteins exhibiting less than seven transmembrane domains, the respective encoding gene […]

ConPred institution(s)
Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki, Japan

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