28th November 2023

Welcome to the LU-Fold workshop!

Presentation slides: https://drive.google.com/file/d/1E3Qpp4TFE-2a8hCI0ynJLGIM5UCUAHB7/view?usp=sharing

Practical worksheet and web tool cheat sheet: https://docs.google.com/document/d/1vQKocMETZ5c01o-ODextqSoK9oTb7gxZ-eDlEp3pe54/edit?usp=sharing

Schedule:

9.00:

• Theory 1: predicting domains and structures
• Leg stretcher and fika
• Tutorial 1: domains and ColabFold, visualisation with PyMOL
• Hands on practicals and flexible lunch break

13.00:

• Theory 2: what is this structure like? 
• Leg stretcher
• Tutorial 2: ESMFold and FoldSeek
• Hands on practicals with worksheet and own proteins 
• Flexible home time

Useful links:

• PyMol for viewing protein structures. This is the preferred viewer for this workshop.
  • Free for course participants at www.pymol.org/edu
  • Register as a student, get code from email and download PyMol and license
  • Tip for exporting structure image: type: ray 1000, 1000. Then export image as png 
• Mol* https://molstar.org/viewer/ an alternative browser-based viewer for protein structures if PyMOL installation is not possible.
• HHPred https://toolkit.tuebingen.mpg.de/tools/hhpred a sequence-based method for sensitive prediction of domains and similarity to proteins with available structures
• AlphaFold structures at the EBI https://alphafold.ebi.ac.uk/ small but constantly growing collection of pre-computed AlphaFold structures
• AlphaFold2 run via colab notebook. NB you will need to be able to sign into a Google account https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
  • To run, click Runtime in the menu, and then run all
  • Raw seq, not Fasta format
  • To co-fold, add a colon between the seqs, eg MMSPQQEE:MKLLLPGFYRRK
• ESMFold https://esmatlas.com/resources?action=fold like AlphaFold2, an AI-based structure prediction method sequence, but does not use multiple sequence alignments. Faster than AlphaFold2, at the cost of accuracy.
• FoldSeek https://search.foldseek.com/search for predicting structures with ESMFold and  finding proteins with similar structures
• Dali http://ekhidna2.biocenter.helsinki.fi/dali/ for searching for structural homologues and aligning structures
• Consurf for colouring structures by sequence conservation (currently the server is down for maintenance but will hopefully return!) https://consurf.tau.ac.il/