Update index.md

workshops/Modeller/index.md

@@ -1,43 +1,52 @@
-# Workshop: Protein structure modelling in Modeller
+# Workshop: Protein structure modeling in Modeller, CollabFold, SwissModel
 
 ## Description
 - We will obtain protein structure based on templates
 - Duration: 60 minutes
 - Objectives: be able to 
-    - Prepare protein sequences for Modeller.
-    - Select a template based on sequence identity comparison.
+    - Prepare protein sequences for Modeller
+    - Select a template based on sequence identity comparison
     - Align target sequence with the template
-    - Model building.
-    - Model evaluation.
-    - CollabFold usage 
-    - AlphaFold2 application using ChimeraX 
+    - Model building
+    - Model evaluation
+    - CollabFold usage
+    - Swiss-Model usage
 
 ## Jupyter notebook
 - [modeller.ipynb](modeller.ipynb)
 
 ## AlphaFold2  
+- [Collab notebook](https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb)
 - [CollabFold paper](https://www.biorxiv.org/content/10.1101/2021.08.15.456425v2)
 - [ChimeraX example](https://www.youtube.com/watch?v=le7NatFo8vI&ab_channel=UCSFChimeraX)
 
+## Swiss-Model  
+- [Web server](https://swissmodel.expasy.org/)
+
 ## Required software and resources
-- Access to a Jupyter notebook evironment with Python 3, modeller, MDanalysis, nglview, Bio libraries
-- Access to Newton cluster
-- Access to Google collab with GPUs 
+- Access to a Jupyter notebook evironment with Python 3, modeller, MDanalysis, nglview, Bio libraries 
+- Access to Google collab with GPUs
+- To install modeller run in your conda environment "conda install -c salilab modeller", use license key "MODELIRANJE"
 
 ## Learning resources
-- [Tutorials](https://salilab.org/modeller/tutorial/)
+- [Modeller tutorial](https://salilab.org/modeller/tutorial/)
+- [Swiss-Model tutorial](https://swissmodel.expasy.org/docs/examples)
 - [DOPE (Discrete Optimized Protein Energy) method](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242414/pdf/2507.pdf)
 
 ## Assignments
-
-Modeller (based on tutorial)
-1. Build model for lactate dehydrogenase from Trichomonas vaginalis (TvLDH) based on a single template. Perfom loop refine by LoopModel, DopeLoopModel. 
-2. Compare plots of energy score (DOPE) for model, template, model with auto loop refine, model with Dope loop refine.
+Select YOUR PROTEIN sequence for modeling structure
+1. Find protein of your interest, [BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) it with "NON-REDUNDANT PROTEIN SEQUENCES" database and choose a sequence with 60% identity or less.
+2. BLAST the chosen sequence with "PROTEIN DATA BANK PROTEINS" database to check if it contains the 3D structure for your sequence (it must NOT have 3D structure in PDB).
 
 AlphaFold2 
-1. Predict 3D structure of your protein (choose small one or fragment); use one of ChimeraX or Collab. Add sequence coverage plot and structure image.  
+1. Predict 3D structure of YOUR PROTEIN (choose small one or fragment); use one of ChimeraX or Collab. Add sequence coverage plot and structure image.  
 
+Swiss-Model
+1. Predict 3D structure of YOUR PROTEIN. Compare with AlphaFold2 structure. Do NOT use AlphaFold structures as a template, only experimental ones!
+
+Modeller (based on tutorial)
+1. Build model for any protein of your interest based on a single template. Perfom loop refine by LoopModel and DopeLoopModel if possible.
 
 ### Troubleshooting
 - Consult with the seminar protocol/recording
-- Ask questions in Slack
+- Ask questions in Telegram