Dear Students,
In exercise 2(ii) of the project, you are asked to use the Dali tool( http://ekhidna.biocenter.helsinki.fi/dali/).
For Dali two very good references are (especially the first one is very interesting):
(a) Liisa Holm, Using Dali for Protein Structure Comparison, Structural Bioinformatics: Methods and Protocols. 2020, Gáspári, Z. (ed.). Humana press, Vol. 2112. p. 29-42 14 p. ( Methods in Molecular Biology; vol. 2112). (an initial version accessible from https://helda.helsinki.fi/items/f56abed3-eb09-48f6-a2f6-e0816090e399)
(b) Liisa Holm: Dali server: structural unification of protein families. Nucleic Acids Res. 50(W1): 210-215 (2022) (accessible fromhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252788/)
and apparently the tutorials of the tool:
http://ekhidna2.biocenter.helsinki.fi/dali/DaliTutorial.pdf
http://ekhidna2.biocenter.helsinki.fi/dali/DaliTutorial2022.pdf
and the website with relevant references:http://ekhidna2.biocenter.helsinki.fi/dali/
Also in https://biologicalmodeling.org/coronavirus/home website you can find answers to similar (but not identical) questions. On the same website, there is also relevant material for protein structure comparison algorithms: https://biologicalmodeling.org/coronavirus/accuracyThis material allows you to use, if you want, other tools for comparing protein structures, in addition to Dali.
Kind regards,
Christos Makris
