Tag: Stability

ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

ENCoM – Exploring Protein Conformational Space and Effect of Mutations on Protein Function and Stability

ENCoM

:: DESCRIPTION

ENCoM is a coarse grained normal modes analysis method to evaluate thermostability of proteins.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ENCoM

:: MORE INFORMATION

Citation

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.
Frappier V, Chartier M, Najmanovich RJ.
Nucleic Acids Res. 2015 Apr 16. pii: gkv343.

ELASPIC – Ensemble Learning Approach for Stability Prediction of Interface and Core Mutations

ELASPIC

:: DESCRIPTION

ELASPIC constructs homology models of domains and domain-domain interactions, and uses those models, together with sequential and other features, to predict the energetic impact of a mutation on the stability of a single domain or the affinity between two domains.

::DEVELOPER

Kim Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ELASPIC

:: MORE INFORMATION

Citation

ELASPIC web-server: proteome-wide structure based prediction of mutation effects on protein stability and binding affinity.
Witvliet D, Strokach A, Giraldo-Forero AF, Teyra J, Colak R, Kim PM.
Bioinformatics. 2016 Jan 21. pii: btw031.

staRank 1.28.0 – Ranking Variables based on their Stability

staRank 1.28.0

:: DESCRIPTION

staRank is an R package for ranking variables based on their stability.Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  staRank

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 17. [Epub ahead of print]
Stability of gene rankings from RNAi screens.
Siebourg J, Merdes G, Misselwitz B, Hardt WD, Beerenwinkel N.

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