Update index.md

workshops/Modeller/index.md

@@ -1,4 +1,4 @@
-# Workshop: Protein structure modelling in Modeller, CollabFold, SwissModel
+# Workshop: Protein structure modeling in Modeller, CollabFold, SwissModel
 
 ## Description
 - We will obtain protein structure based on templates
@@ -34,11 +34,14 @@
 - [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 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.