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DeltaGREM

Computes the folding free energy of proteins with known structure and sequence. Sequences can be input either through a Multiple Sequence Alignment including the sequence of at least one of the input PDB or through a list of mutations.

The folding free energy takes into account the native state as represented in one of the input PDB files, the unfolded state, and the misfolded state (compact conformations dissimilar from the native), modelled as a Random Energy Model (REM) up to the second (REM2) or third (REM3) moment of the contact energy.

References:

  1. For the model of the misfolded state: Minning J, Porto M, Bastolla U. Detecting selection for negative design in proteins through an improved model of the misfolded state. Proteins. 2013 81:1102-12.
  2. For the numerical computation of the REM free energy: Arenas M, Sánchez-Cobos A, Bastolla U. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. Mol Biol Evol. 2015 32:2195-207.
  3. For the complete model: Bastolla U. Detecting selection on protein stability through statistical mechanical models of folding and evolution. Biomolecules. 2014 4:291-314.

  • Usage and installation Documentation included with the package.
  • License : Free use for Educational and Research Purposes.
  • Contact : ub@cbm.uam.es
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