:: DESCRIPTION
TMKink is a method to predict transmembrane helix kinks.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Protein Sci. 2011 Jul;20(7):1256-64. doi: 10.1002/pro.653. Epub 2011 Jun 2.
TMKink: a method to predict transmembrane helix kinks.
Meruelo AD1, Samish I, Bowie JU.
:: DESCRIPTION
HelixCorr is a software to predict correlated mutations specifically for the transmembrane parts of membrane proteins. It includes predictions obtained by several individual prediction algorithms and combines them to a consensus prediction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 Dec 15;23(24):3312-9.
Co-evolving residues in membrane proteins.
Fuchs A, Martin-Galiano AJ, Kalman M, Fleishman S, Ben-Tal N, Frishman D.
:: DESCRIPTION
COMSAT is a Support-Vector-Machine (SVM) and Mixed-Integer-Linear-Programming (MILP) based method for residue contact prediction in helical transmembrane proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming.
Zhang H, Huang Q, Bei Z, Wei Y, Floudas CA.
Proteins. 2016 Mar;84(3):332-48. doi: 10.1002/prot.24979.
:: DESCRIPTION
HMMpTM is a Hidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence.
::DEVELOPER
The Biophysics and Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Biochim Biophys Acta. 2014 Feb;1844(2):316-22. doi: 10.1016/j.bbapap.2013.11.001. Epub 2013 Nov 10.
HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.
Tsaousis GN, Bagos PG, Hamodrakas SJ.
:: DESCRIPTION
HMM-TM is a Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information.
::DEVELOPER
The Biophysics and Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2006 Apr 5;7:189.
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins.
Bagos PG, Liakopoulos TD, Hamodrakas SJ.
:: DESCRIPTION
PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices.
::DEVELOPER
Laboratory of biomolecular modeling.
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 15;30(6):889-90. doi: 10.1093/bioinformatics/btt645.
PREDDIMER: a web server for prediction of transmembrane helical dimers.
Polyansky AA1, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.
:: DESCRIPTION
SOMRuler is a novel TMH predictor with excellent interpretability while possessing high prediction accuracy.
::DEVELOPER
Computational Systems Biology Group, Shanghai Jiao Tong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
IEEE Trans Nanobioscience. 2011 Jun;10(2):121-9. doi: 10.1109/TNB.2011.2160730. Epub 2011 Jul 7.
SOMRuler: a novel interpretable transmembrane helices predictor.
Yu D, Shen H, Yang J.
:: DESCRIPTION
transFold is a web server for beta-barrel supersecondary structure prediction. Unlike other software which employ machine learning methods, transFold uses multi-tape S-attribute grammars to describe the space of all possible supersecondary structures, then applies dynamic programming to compute the global energy minimum structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
J. Waldispühl, B. Berger, P. Clote, J.-M. Steyaert,
TransFold: a Web Server for predicting the structure and residue contacts of transmembrane beta-barrels,
Nucleic Acids Res. 34(Web Server Issue):189-193 (2006).
:: DESCRIPTION
TMhhcp is developed to predict residue-residue contacts in alpha-helix transmembrane proteins. The predicted contacts could be further used to predict helix-helix interactions between helices.
::DEVELOPER
Ziding Zhang’s Lab, China Agricultural University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2011;6(10):e26767. doi: 10.1371/journal.pone.0026767. Epub 2011 Oct 28.
Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach.
Wang XF1, Chen Z, Wang C, Yan RX, Zhang Z, Song J.
:: DESCRIPTION
TBBpred predicts the whether a protein is outer membrane betat-barrel protein or not. It also predicts transmembrane Beta barrel regions in a given protein sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Natt, N.K., Kaur, H. and Raghava, G. P. S. (2004)
Prediction of Transmembrane regions of beta-barrel proteins using ANN and SVM based method.
Proteins: Structure, Function, and Bioinformatics 56:11-8