TMhit statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

TMhit specifications

Information


Unique identifier OMICS_20712
Name TMhit
Alternative name TM helix– helix interaction prediction
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data Protein sequence(s).
Input format FASTA
Computer skills Basic
Stability No
Maintained No

Maintainers


This tool is not available anymore.

Publication for TM helix– helix interaction prediction

TMhit citations

 (5)
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

[…] fferences between TM and globular interaction motifs , , , . For example, the helix–helix interaction prediction performance for five predictors (the TM protein contact predictors MEMPACK, TMHcon and TMhit, and the globular protein contact predictors PROFcon and SVMcon) was assessed based on a data set of 74 sequences, which contained at least two TM helices . The TM proteins' specific predictors […]

library_books

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data

2015
PLoS One
PMCID: 4546402
PMID: 26291722
DOI: 10.1371/journal.pone.0135455

[…] The interactions between transmembrane helix-helix pairs in bilitranslocase were predicted using the open-source IMP program (http://integrativemodeling.org) [] as well as the TMhit web server [].The IMP predictions take into account the complete transmembrane regions and not the individual residues. In this case, the BTL transmembrane region sequences with defined topologi […]

library_books

Probabilistic grammatical model for helix‐helix contact site classification

2013
PMCID: 3892132
PMID: 24350601
DOI: 10.1186/1748-7188-8-31

[…] me group predicted contacts between residues with 26% accuracy using a neural network approach []. This resulted in 78% accuracy in helix‐helix contact prediction. Lo et al.[] developed the webserver TMhit, which predicts membrane protein topology using a support vector machine. Later, they designed a framework for prediction of helix‐helix interactions in membrane proteins from residue contacts, […]

library_books

Conserved residue mutations in Wzy affect O antigen polymerization and Wzz mediated chain length regulation in Pseudomonas aeruginosa PAO1

2013
Sci Rep
PMCID: 3854497
PMID: 24309320
DOI: 10.1038/srep03441

[…] E-value inclusion threshold of 10−6, resulting in a final MSA of 30 aligned sequences. Based on the MSA, amino acid sequence logos were generated using WebLogo (http://weblogo.berkeley.edu/logo.cgi). TMhit analysis (L/2 threshold) was performed online (http://bio-cluster.iis.sinica.edu.tw/TMhit/), with topological restraints introduced based on the published TMS boundaries for the WzyPa topology m […]

library_books

A cationic lumen in the Wzx flippase mediates anionic O antigen subunit translocation in Pseudomonas aeruginosa PA01

2012
Mol Microbiol
PMCID: 3412221
PMID: 22554073
DOI: 10.1111/j.1365-2958.2012.08084.x

[…] nsity for each membrane domain to form contacts with others was examined to gain insights into the manner in which they may pack relative to each other. This was accomplished using the MEMPACK () and TMhit () support vector machine classification approaches, which minimize the over-fitting of data (). These analyses indicated that TMS3, 4, 9, 11 and 12 possessed a high number of potential contacts […]

Citations

Looking to check out a full list of citations?

TMhit institution(s)
Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Bioinformatics and Structural Biology, Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan; Bioinformatics Laboratory, Institute of Information Science, Academia Sinica, Taipei, Taiwan; Centre for Cancer Biomedicine, University of Oslo, Oslo; SAMBA, Norwegian Computing Center, Oslo, Norway
TMhit funding source(s)
Supported by Thematic Program of Academia Sinica (grant number AS95ASIA03); National Science Council (grant number NSC 97- 2627-P-001-004, in part).

TMhit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review TMhit