TBBpred – Transmembrane Beta Barrel prediction

TBBpred

:: 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

TBBpred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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

HMM-TM – Prediction of Transmembrane Alpha-Helical Proteins

HMM-TM

:: 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

  • Web browser

:: 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.

HMMpTM – Transmembrane Protein Topology Prediction using Phosphorylation and Glycosylation Site Prediction

HMMpTM

:: 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

  • Web browser

:: 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.

COMSAT – Residue Contact Prediction for Transmembrane Proteins

COMSAT

:: 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

COMSAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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.

TMhhcp – Transmembrane Helix-Helix Contact Predictor

TMhhcp

:: 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

  • Web Browser

:: DOWNLOAD

 NO

:: 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.

SOMRuler – A Novel Interpretable Transmembrane Helices Predictor

SOMRuler

:: 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

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 SOMRuler

:: 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.

PREDDIMER – Prediction tool for an Ensemble of Transmembrane α-helical Dimer Conformations

PREDDIMER

:: 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

  • Web browser

:: 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.

TMKink – Transmembrane Kink Predictor

TMKink

:: DESCRIPTION

TMKink is a method to predict transmembrane helix kinks.

::DEVELOPER

BOWIE LAB

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: 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.

HelixCorr 20081105 – Predict interacting Transmembrane Helices

HelixCorr 20081105

:: 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

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HelixCorr

:: 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.

transFold – Super-secondary Structure Prediction of Transmembrane β-barrel proteins

transFold

:: 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

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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).