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Protocols

PRED-TMR specifications

Information


Unique identifier OMICS_07261
Name PRED-TMR
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PRED-TMR

PRED-TMR citations

 (21)
library_books

Conditional mouse models support the role of SLC39A14 (ZIP14) in Hyperostosis Cranialis Interna and in bone homeostasis

2018
PLoS Genet
PMCID: 5903675
PMID: 29621230
DOI: 10.1371/journal.pgen.1007321

[…] s substitutions that can occur in the human genome []. As a zinc (Zn) transporter, ZIP14 has six or eight transmembrane domains, depending on the literature or prediction program used (TMHMM, MEMSAT, PRED-TMR, HMMTOP) [, ]. Nevertheless, the p.L441R mutation is always located at the end of the second-to-last transmembrane domain of ZIP14. All transmembrane prediction programs predict the variant t […]

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

[…] hemical methods based on hydrophobicity indexes , , and several hydropathy analyses that identify long stretches of hydrophobic residues are available for the topology prediction of TM helices (KD , PRED-TMR , SOSUI , TM Finder , TopPred2 ) or barrels (BBF , BOMP ). These methods are successful at identifying the hydrophobic core of TM regions, but cannot precisely determine the ends of TM residu […]

call_split

Update on Nox function, site of action and regulation in Botrytis cinerea

2016
PMCID: 5611593
PMID: 28955467
DOI: 10.1186/s40694-016-0026-6
call_split See protocol

[…] y.com/berry.phtml?topic=protcompan&group=help&subgroup=proloc), transmembrane regions were predicted by using the programs TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) and SACS MEMSAT2 [] as well as PRED-TMR []. […]

library_books

Isolation of New Gravitropic Mutants under Hypergravity Conditions

2016
Front Plant Sci
PMCID: 5040707
PMID: 27746791
DOI: 10.3389/fpls.2016.01443

[…] n auxin influx carrier protein that plays a role in differential growth during gravitropism through the modulation of polar auxin transport (). In AUX1, 11 transmembrane regions were predicted by the PRED-TMR2 software, and the SNP (Gly381Asp) was identified in the 10th transmembrane region.Single aux1 mutants exhibit reduced gravitropism in primary roots (; ), and normal phototropism in hypocotyl […]

call_split

The Signature Sequence Region of the Human Drug Transporter Organic Anion Transporting Polypeptide 1B1 Is Important for Protein Surface Expression

2014
PMCID: 4209838
PMID: 25371825
DOI: 10.1155/2014/129849
call_split See protocol

[…] ing 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 the OATP1B1 sequence on the known structure of GlpT [ […]

library_books

A Comprehensive Phylogenetic and Structural Analysis of the Carcinoembryonic Antigen (CEA) Gene Family

2014
Genome Biol Evol
PMCID: 4079198
PMID: 24858421
DOI: 10.1093/gbe/evu103

[…] he outputs of the search engines available in SMART v.7 (), PFAM v.27 () and CDD v.3 () and InterPro v.42 () protein signature databases. The TM regions were predicted with the programs MINNOU () and PRED-TMR2 (). […]

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PRED-TMR institution(s)
Faculty of Biology, Department of Cell Biology and Biophysics, University of Athens, Panepistimiopolis, Athens, Greece

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