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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.
Bd. 46
(2025)
Heft 17
.
- e70160.
ISSN 1096-987X
DOI: https://doi.org/10.1002/jcc.70160
Abstract
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.
Weitere Angaben
| Publikationsform: | Artikel in einer Zeitschrift |
|---|---|
| Begutachteter Beitrag: | Ja |
| Institutionen der Universität: | Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Lehrstuhl Biochemie III - Proteindesign > Lehrstuhl Biochemie III - Proteindesign - Univ.-Prof. Dr. Birte Höcker Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Lehrstuhl Biochemie III - Proteindesign |
| Titel an der UBT entstanden: | Ja |
| Themengebiete aus DDC: | 500 Naturwissenschaften und Mathematik > 540 Chemie |
| Eingestellt am: | 01 Jul 2025 05:08 |
| Letzte Änderung: | 01 Jul 2025 05:08 |
| URI: | https://eref.uni-bayreuth.de/id/eprint/94021 |