Table 1.
Timeline of methods for Hsp70 binding site prediction and their key insights. The acronym PSSM stands for Position-specific Scoring Matrix. They are 20 by N matrices (20 amino acids, N substrate residues) and are often given in energy units, so that each element in the matrix is the binding affinity per amino acid and substrate position.
| Model or Authors | Year | Chaperone | Key features and insights | Online tool/code | Citation |
|---|---|---|---|---|---|
| Blond-Elguindi et al. | 1993 | BiP | PSSM based on sequence statistics | -- | 42,65 |
| Gragerov et al.; Ivey et al. | 1994 | DnaK | Binding analysis from random peptide phage display. | -- | 43,44 |
| Rüdiger et al. | 1997 | DnaK | Identification of the canonical binding motif | -- | 45 |
| Rüdiger et al.; Srinivasan et al. | 2001; 2012 | DnaJ | DnaJ and DnaK share many targets | -- | 46,66 |
| LIMBO | 2009 | DnaK | FoldX 49 and Structure-based PSSM improves transferability of sequence-based PSSM | https://limbo.switchlab.org/ | 55 |
| BiPPred | 2016 | BiP | MD-based PSSM requires minimal training and no sequence-based PSSM | https://www.bioinformatics.wzw.tum.de/bippred/submit/ | 60 |
| ChaperISM | 2019 | DnaK | Position-Independent Scoring Matrix (PISM) improves agreement with binding array data | https://github.com/BioinfLab/ChaperISM | 56 |
| Paladin | 2021 | DnaK | MD-based PSSM, substrate register and orientation prediction | https://github.com/enordquist/paladin | 41 |