at Google ScholarTitle data
Ayyildiz, Merve ; Noske, Jakob ; Gisdon, Florian J. ; Kynast, Josef ; Höcker, Birte:
Evaluation of Physics-Based Protein Design Methods for Predicting Single Residue Effects on Peptide Binding Specificities.
In: Journal of Computational Chemistry.
Vol. 46
(2025)
Issue 17
.
- e70160.
ISSN 1096-987X
DOI: https://doi.org/10.1002/jcc.70160
Abstract in another language
Understanding the interactions that make up protein–protein or protein-peptide interfaces is a crucial step towards applications in biotechnology. The mutation of a single residue can have a strong impact on binding affinity and specificity, which is difficult to capture in sampling and scoring. Many established computational methods provide an estimate of binding or non-binding; however, comparing highly similar ligands is an important and significantly more challenging problem. Here we evaluated the capability of predicting ligand binding specificity using three established but conceptually different physics-based methods for protein design. As a model system, we analyzed the binding of peptides to designed armadillo repeat proteins, where a single residue of the peptide was changed systematically, leading to affinity changes in the range of 1–1000 nM. We critically assessed the prediction accuracy of the computational methods. While a good correlation with experimentally determined data was observed in several cases, specific biases in the prediction performance of each method were identified.
Further data
| Item Type: | Article in a journal |
|---|---|
| Refereed: | Yes |
| Institutions of the University: | Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry III - Protein Design > Chair Biochemistry III - Protein Design - Univ.-Prof. Dr. Birte Höcker Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry III - Protein Design |
| Result of work at the UBT: | Yes |
| DDC Subjects: | 500 Science > 540 Chemistry |
| Date Deposited: | 01 Jul 2025 05:08 |
| Last Modified: | 01 Jul 2025 05:08 |
| URI: | https://eref.uni-bayreuth.de/id/eprint/94021 |