Bioinformatics tools for disordered proteins
Predictor |
Principle |
IUPred | estimated interaction energy |
GlobPlot | single AA propensity |
DISOPRED2 | SVM + NN for smoothing |
PONDR® VSL2 | SVM |
PONDR-FIT | Meta server based on NN |
Predisorder | 1-D recursive NN with profiles |
CSpritz | SVM with non-linear kernel |
FoldIndex© | AA propensities |
RONN | bio-basis function neural network |
DRIP-PRED | self-organizing maps |
DisPSSM (iPDA) | two-stage classifier of Radial Basis Function Networks (RBFN) |
POODLE (S, L, W, I) | SVM with physicochemical properties |
UCON | Low contact density |
MD | Meta-predictor |
PrDOS | SVM + homology |
OnD-CRF | Conditional random fields |
DISOclust | 3D structural models |
Databases:
- Disprot: Database of experimentally verified disordered proteins
- ELM: Database of eukarotic linear motifs
- PDB: 3D Structural database of proteins
- BMRB: Biological Magnetic Resonance Data Bank
Additional Tools and Resources:
- ANCHOR: Server for predicting disordered binding regions in proteins
- UniProt: Protein sequence database
- Pfam: Domain database
- SMART: Domain database
- PDBsum: Annotated 3D structures of proteins
- COILS: Coil prediction
- BLAST: Similarity searches
- Jpred: Secondary structure prediction
- ProtParam: Sequence analysis
- The webpage of the ITC training course on protein aggregation
- TANGO: Prediction of beta-aggregation in protein sequences
- WALTZ: Prediction of amyloid forming segments in protein sequences
- FoldX plugin for YASARA: Calculate free energy changes of point mutations in protein structures
- ClustalW2: Multiple sequence alignment tool
- Random coil chemical shifts for intrinsically disordered proteins
- Translate: Translate DNA into protein sequence
- K2D3: Estimates protein secondary structure from CD spectra
- Disphos: Disorder-Enhanced Phosphorylation Sites Predictor
- Oligo Calc: Oligonucleotide Properties Calculator
- Metalweb: access to the knowledge on metalloproteins