General Information
| Description | Towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies |
| Homepage | http://www.iitm.ac.in/bioinfo/GAP/ |
Publications
GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies
Motivation:
Distinguishing between amyloid fibril-forming and amorphous β-aggregating aggregation-prone regions (APRs) in proteins and peptides is crucial for designing novel biomaterials and improved aggregation inhibitors for biotechnological and therapeutic purposes.
Results:
Adjacent and alternate position residue pairs in hexapeptides show distinct preferences for occurrence in amyloid fibrils and amorphous β-aggregates. These observations were converted into energy potentials that were, in turn, machine learned. The resulting tool, called Generalized Aggregation Proneness (GAP), could successfully distinguish between amyloid fibril-forming and amorphous β-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.
Conclusion:
Accuracies of the predictions made by GAP are significantly improved compared with other methods capable of predicting either general β-aggregation or amyloid fibril-forming APRs. This work demonstrates that amino acid side chains play important roles in determining the morphological fate of β-mediated aggregates formed by short peptides.
Availability and implementation:
http://www.iitm.ac.in/bioinfo/GAP/ .
Contact:
gromiha@iitm.ac.in
Supplementary information:
Supplementary data are available at Bioinformatics online.
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