Tag: Beta Sheet

BCov 1.0 – Predicting Protein beta-sheets from Sequence

BCov 1.0

:: DESCRIPTION

BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence. BCov is based on the PSICOV residue contact predictor, dynamic-programming algorithm for beta-strand alignments and integer programming for beta-sheet topology prediction.

::DEVELOPER

Castrense Savojardo, Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BCov

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 15;29(24):3151-7. doi: 10.1093/bioinformatics/btt555. Epub 2013 Sep 23.
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.
Savojardo C1, Fariselli P, Martelli PL, Casadio R.

BETApro 1.0 – Protein Beta Sheet Predictor

BETApro 1.0

:: DESCRIPTION

BETApro is a software of prediction of beta-residue pairs, beta-strand pairs, strand alignment, pairing direction, and beta-sheet topology.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BETApro

:: MORE INFORMATION

Citation:

Jianlin Cheng and Pierre Baldi,
Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms,
Bioinformatics, vol. 21(Suppl 1), pp. i75-84, 2005.

Betascan 20081027 – Predict Beta-sheets from Sequence alone using Pairwise Probabilistic Modeling

Betascan 20081027

:: DESCRIPTION

BETASCAN calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence’s potential beta-structures.

::DEVELOPER

Bonnie Berger , Susan Lindquist , Lenore Cowen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 Betascan

:: MORE INFORMATION

Citation:

BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.
Bryan AW Jr, Menke M, Cowen LJ, Lindquist SL, Berger B.
PLoS Comput Biol. 2009 Mar;5(3):e1000333. doi: 10.1371/journal.pcbi.1000333.