Tag: beta-barrel

BetAware – Beta-Barrel Detection and Topology Prediction

BetAware

:: DESCRIPTION

BETAWARE is a software package designed for the analysis of trans-membrane beta-barrel proteins.

::DEVELOPER

Castrense Savojardo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • python argparse library
  • python numpy

:: DOWNLOAD

  BetAware

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):504-5. doi: 10.1093/bioinformatics/bts728. Epub 2013 Jan 6.
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Savojardo C, Fariselli P, Casadio R.

BOCTOPUS 2.0 – Topology Predictor for Beta-barrel Membrane Proteins

BOCTOPUS 2.0

:: DESCRIPTION

BOCTOPUS allows for requests of up to 1 protein sequence at a time for better predictive performance.

::DEVELOPER

Elofsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • cmake.

:: DOWNLOAD

 BOCTOPUS

:: MORE INFORMATION

Citation

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A.
Bioinformatics. 2016 Jan 21. pii: btw025.

Bioinformatics. 2012 Feb 15;28(4):516-22. doi: 10.1093/bioinformatics/btr710. Epub 2012 Jan 13.
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.
Hayat S1, Elofsson A.

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

BOMP – The beta-barrel Outer Membrane Protein Predictor

BOMP

:: DESCRIPTION

BOMP is a tool for prediction of beta-barrel integral outer membrane proteins (BOMPs). The user may submit a list of proteins, and receive a list of predicted BOMPs.

::DEVELOPER

Uni Computing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Berven FS, Flikka K, Jensen HB, Eidhammer I.
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria .
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9