Help Privacy Policy Disclaimer
  Advanced SearchBrowse




Meeting Abstract

Coiled-coil domains and AlphaFold2: friends or foes?


Dunin-Horkawicz,  S       
Department Protein Evolution, Max Planck Institute for Biology Tübingen, Max Planck Society;

Fulltext (restricted access)
There are currently no full texts shared for your IP range.
Fulltext (public)
There are no public fulltexts stored in PuRe
Supplementary Material (public)
There is no public supplementary material available

Madaj, R., Kamiński, K., Wiński, A., Ludwiczak, J., & Dunin-Horkawicz, S. (2022). Coiled-coil domains and AlphaFold2: friends or foes? In 8th Alpbach Workshop: Coiled Coil, Fibrous and Repeat Proteins (pp. 21).

Cite as: https://hdl.handle.net/21.11116/0000-000B-6DF8-4
Deep learning-based tools revolutionized the field of protein structure prediction. We present our recent attempts to use one of such methods, AlphaFold2 (AF2), for the modeling of coiled-coil domains. We benchmarked AF2 using a set of experimental coiled-coil structures. For each benchmark case, we applied the following procedure: first, we determined local structural parameters [1] for the experimental structure and the corresponding AF2 model. Then, by comparing these structural parameters, we defined a quality index that reflects the discrepancy between the experimental structure and the model. Knowing the advantages and limitations of AF2, we performed more focused analyses of (i) HAMP domains [2], a family of coiled coils whose conformational changes are key for prokaryotic signal-transducing proteins, and (ii) the applicability of AF2 models for the augmentation of data sets used for training of machine learning methods.