Biophysical predictions

Research project Biophysical predictions

Predicting biophysical characteristics of proteins from their amino acid sequence

Most methods that predict per-residue characteristics from sequence are trained on information from in silico protein structures, which do not necessarily capture how the protein behaves in solution (e.g. helix fraying, loop movements). We are developing prediction approaches that are based on estimations of dynamics and conformation directly from experimental NMR data. These estimations are less accurate but can encompass the whole range of protein behaviour, from intrinsically disorded via molten globule to fully folded. This is the basis of the DynaMine method published at the end of 2013. We have evidence that the predictions add a new, physical, dimension to the protein sequence that has many uses, such as improving sequence alignment or detecting early folding events - areas currently under investigation.

Funding

G.0328.16N (Jan. 1, 2016-Dec. 31, 2019)
FoldMod - The role of local amino acid interactions in the folding of proteins, the stability of their fold and the location of post-translational modifications.

BB2B 2010-1-12 (Dec. 1, 2010-Nov. 30, 2015)
Brains Back to Brussels project - Combining experiment and informatics to study biopolymer dynamics and interactions.

Resources

DynaMine (Software tool, In-house)

ST resource  DynaMine
Prediction of protein backbone dynamics from sequence only

EFoldMine (Software tool, In-house)

ST resource  EFoldMine
Prediction of protein early folding regions from sequence only

DisoMine (Software tool, In-house)

ST resource  DisoMine
Prediction of protein disorder from sequence only

Start2Fold (Database, In-house)

DB resource  Start2Fold
Database with information on the early/intermediate/late folding regions of proteins, and their unfolding, from hydrogen/deuterium exchange data from NMR and X-ray crystallography

AmyPro (Database, External collaboration)

DB resource  AmyPro
AmyPro is a database with information on aggregating regions of proteins.

RINspector (Software tool, External collaboration)

ST resource  RINspector
RINspector is a CytoScape app that combines protein-structure based network analysis with DynaMine predictions

PhyloCys (Software tool, In-house)

ST resource  PhyloCys
PhyloCys is a tool to predict cysteine disulphide bonding patterns in proteins from evolutionary sequence information.

Sephiroth (Software tool, In-house)

ST resource  Sephiroth
Sephiroth is a tool to predict the cysteine disulphide bonding pattern in proteins from evolutionary sequence information.

SeRenDIP (Software tool, External collaboration)

ST resource  SeRenDIP
Sequence-based Homo- and Heteromeric Protein-protein Interaction sites prediction using Random Forest; a key feature of this method are the DynaMine predictions

DisProt 7.0 (Database, External collaboration)

DB resource  DisProt 7.0
DisProt is a database with annotations on disordered regions of proteins based on experimental observations.

MobiDB (Database, External collaboration)

DB resource  MobiDB
MobiDB is a database of (predicted) annotations on protein disorder and mobility