A train-the-trainer workshop as a satellite event of the Annual International Conference of the RSBMB 2024

Slide handouts

Preamble: come prepared

Bring your computer.
A tablet may work for some things, but not fully functional

While you are at home:

• Install Java (unless you already have it) https://java.com
• Download Jmol [direct link for version 16.2.25] or go to https://jmol.sourceforge.net/, follow links “Download Jmol+JSmol”, get the **-binary.zip file (62 MB)
  Extract (unzip) just the Jmol.jar file (there is no instalation, just keep that file at hand)
• Alternative smaller download (minimal package 10 MB): https://biomodel.uah.es/Jmol-16.2.25.zip
  Extract (unzip) the Jmol.jar file

1. Come to class with a molecule in your pocket

(Live demo)

2. OK, but... Where do I get the molecule?

Databases:

• PDB @ USA (RCSB) rcsb.org (macromolecules) Example 8PJA
• PDB @ Europe (PDBe) pdbe.org (macromolecules) Example 8PJA
• PubChem pubchem.org (smaller molecules) Example NADPH

Server: Chemical Identifier Resolver “CACTUS”, NCI (NIH) cactus.nci.nih.gov/chemical/structure (smaller molecules)

Database connection: directly from Jmol: Database_Connection

1b. So, now, let’s do it yourselves

(practice)

3. Use Proteopedia as a ready-made platform

Example of seeded page:

• https://proteopedia.org/w/8pja

Examples of authored pages:

• https://proteopedia.org/w/Aldehyde_Dehydrogenase
• https://proteopedia.org/w/Nitrogenase
• Proteopedia:Table of Contents

4. 3D structure prediction

Databases:

• AlphaFoldDB
• ESM Metagenomic Atlas

Prediction of folding:

• NCBI protein
• ESM Fold sequence

Saving results of ESMFold

Colouring ESMfold results by confidence:

• Auxiliary tool: https://biomodel.uah.es/Jmol/fold_AI/

5. Authoring Proteopedia

Proteopedia, life in 3D: a collaborative & free 3D-encyclopedia of proteins & other biomolecules.

Proteopedia Take Home Guidelines