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2) Perform homology modelling via web server: SWISS-MODEL.

Describe what you have done for this step. Discuss the table of templates SWISS- MODEL returns. Identify any promising templates to be taken further to perform modelling of your target, and explain your selection.
(Hint 1: select at least 1 template here for automated homology modelling.)
3) Examine the model(s) created by the server. Download the PDB file(s) for the template(s) used by the server, as well as the PDB file(s) of the model(s) created by the server.
(Save these results, as well as any evaluation plots/statistics SWISS-MODEL returns for your model you will need them later in this assignment.)

4) Perform a BLAST search with the target sequence for structure modelling (using the PDB database of protein structures). Retrieve sequences of suitable templates.

Describe the BLAST results.
(max. 250 words)
5) From your BLAST search, select the best template(s) for homology modelling.

(Hint: select at least 1 template from the BLAST table.)

Describe which template(s) you have selected, and justify your selection.
6) Perform T-Coffee alignments of your query sequence and the selected templates.

Compare the template(s) hits returned from SWISS-MODEL in step (2), and the one(s) you would have selected based on BLAST and the T-Coffee alignments. Are there any notable differences between T-coffee alignments and SWISS-MODEL alignments and how are these explained?

7) Perform your search for a 3D model via Alphafold2- extract the domain you are interested in.
(Save the PDB files of the of the domain/complete protein and explain the Alphafold2 model structure providing the corresponding figures)
8) Examine your models, from both alignment-mode and automated-mode homology modelling using molecular visualisation software (e.g. PyMOL). Perform a comparison (structural, 3D superimposition) with the corresponding templates, and/or any deposited models (e.g. in databases such as Modbase) of your target protein. Analysis in this step can include: i) comparison between the models, ii) comparison between the templates, iii) comparison between the models and the templates. Discuss briefly what each one of these analyses can tell us based on what is relevant for your assigned protein/sequence.

a) Display informative snapshots of your structural analysis. Discuss these results, referring, wherever necessary, to other results you have had so far, e.g. the alignments and the BLAST/SWISS-MODEL template hits table.
b) Evaluate the model(s) from the parameters provided in the output of SWISS-MODEL.
9) Evaluate the model(s) and template structures with Molprobity.

Display results from Molprobity. Discuss these results in light of your structural analyses, as well as your results on the template searches.
10) Search for the functions of your assigned protein.

Using public repositories and servers, as well as any literature you have found, comment on possible functions for the gene/protein corresponding to the selected sequence. Provide the interacting partners of your protein in homo sapiens using STRINGDB. If there is no human homolog use the closest human protein identified in blastp.

This is the fasta sequence
>XX8
QQASATGSISIEEIDLEGKYVQLKNNSEKDQSLGNWRLKRQIGDGEEIAYKFTPKYVLRAQTVTIWGADAGVSHSPPSVLVWKNQGSWGTGGNIRTYLVNSDGEEVAVRTVT

Please can someone provide guidance on how to navigate through these questions. Feeling really stuck

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