Tag: Transmembrane Protein

MemBrain 20200114 – Transmembrane Protein Structure Prediction

MemBrain 20200114

:: DESCRIPTION

MemBrain is a web server developed for transmembrane protein structure prediction. It contains two main prediction functions, i.e., transmembrane helix (TMH) prediction and TMH-TMH residue contact prediction.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

MemBrain: improving the accuracy of predicting transmembrane helices.
Shen H, Chou JJ.
PLoS One. 2008 Jun 11;3(6):e2399. doi: 10.1371/journal.pone.0002399.

MEMSAT-SVM 1.3 – SVM Transmembrane Protein Structure Prediction

MEMSATSVM 1.3

:: DESCRIPTION

MEMSATSVM is a SVM (support vector machines) based TM (Transmembrane Protein) protein topology predictor.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MEMSAT-SVM

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2012 Jul 17;13:169. doi: 10.1186/1471-2105-13-169.
Detecting pore-lining regions in transmembrane protein sequences.
Nugent T1, Jones DT.

Timothy Nugent and David T Jones
Transmembrane protein topology prediction using support vector machines
BMC Bioinformatics 2009, 10:159

DAS-TMfilter – On filtering False Positive Transmembrane Protein Prediction

DAS-TMfilter

:: DESCRIPTION

The modified DAS method, the DAS-TMfilter algorithm, has an unchanged high sensitivity for TM segments ( approximately 95% detected in a learning set of 128 documented transmembrane proteins). At the same time, the selectivity measured over a non-redundant set of 526 soluble proteins with known 3D structure is approximately 99%, mainly because a large number of falsely predicted single membrane-pass proteins are eliminated by the DAS-TMfilter algorithm.

::DEVELOPER

the Institute of Enzymology, Hungarian Academy of Sciences.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DAS-TMfilter

:: MORE INFORMATION

Citation

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.
Cserzo M, Eisenhaber F, Eisenhaber B, Simon I.
Bioinformatics. 2004 Jan 1;20(1):136-7.

MEMSAT 3 – Transmembrane Protein Structure Prediction

MEMSAT 3

:: DESCRIPTION

MEMSAT (MEMbrane protein Structure And Topology) is a program which predicts the secondary structure and topology of all-helix integral membrane proteins based on the recognition of topological models. The original MEMSAT method employed a set of statistical tables (log likelihood ratios) compiled from well- characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. These statistical tables showed definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MEMSAT

:: MORE INFORMATION

Citation

Jones D.T. (2007)
Improving the accuracy of transmembrane protein topology prediction using evolutionary information.
Bioinformatics. 2007 Mar 1;23(5):538-44. Epub 2007 Jan 19.

TOPO2 – Create Transmembrane Proteins Images

TOPO2

:: DESCRIPTION

TOPO2 is an open source program written in Python for the creation of transmembrane protein 2D topology images. It makes no attempt to predict the TMDs that it displays. The user needs to supply that information. Residues of interest can be highlighted, if desired.

TOPO2 Web Version

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • Python

:: DOWNLOAD

TOPO2

:: MORE INFORMATION

Contact Susan Jean Johns (email: johns@cgl.ucsf.edu) for more information about the software or if you are having problems with the site.