Description of the methodology used

Sequence based predictions

The DynaMine backbone and sidechain dynamics and conformational propensities are described in:

The EFoldMine early folding predictions are described in:

The DisoMine disorder predictions are described in:

The Agmata beta-sheet aggregation predictions are described in:

With these predictions we try to capture the 'emergent' properties of the proteins, so the inherent biophysical propensities encoded in the sequence, rather than the behavior of a final folded state. This relevant as proteins are dynamic even when folded, and might not fold at all (as with intrinsically disordered proteins).

These predictions are single-sequence based, and for multiple sequence alignments (MSAs) for a target protein the median/quartile/outlier information in the plots is derived by running the predictions on each sequence separately, mapping them back to the MSA, and looking at the 'biophysical variation' observed in evolution in relation to the residues of the original protein. These are currently not available for Agmata as the method is computationally too expensive.

NMR methods

The ShiftCrypt method calculates, on the basis of NMR chemical shift values for a protein, a single per-residue value that reflects that residues' biophysical behavior. This article contains further examples and information about the meaning of the ShiftCrypt values:

This article contains information on the ShiftCrypt web server and the alignment procedure.