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PDB file format from https://lammpstube.com
A simple, although not always reliable, way to discover the secondary structure of a peptide sequence is to look up a protein with similar primary sequence in a database. Let us try this! The task is to obtain the secondary structure of the following peptide sequence: HYLCKYVINAIPPTLTAKIHFRPELPAERNQLIQRLA
HYLCKYVINAIPPTLTAKIHFRPELPAERNQLIQRLA
Use the above-described procedure to learn most about the following peptide sequence: TEYAINKLRQLYVLRC.
TEYAINKLRQLYVLRC
ESMFold is a deep learning-based method developed for predicting protein tertiary structures from amino acid sequences. In the following steps, we will show how the method works. We will use one of the existing ESMFold predictions and verify it against PDB database.
Predict and validate your own protein structure. The output to be reported:
Test the limits of applicability of the prediction. You can focus on large proteins (such as dynein motor protein 4AKG with multiple interacting domains), disordered proteins, proteins with novel folds, or membrane proteins. However, it becomes more and more difficult to find proteins for which prediction fails. See for example the strengths and limitations of AlphaFold2.
Resources (other from the resources available above):
Abramson et al.: Accurate structure prediction of biomolecular interactions with AlphaFold 3, Nature, 2024 (pdf preprint).
Poleksic: Algorithms for optimal protein structure alignment, Bioinformatics, 2009 (online).