diff --git a/workshops/Modeller/index.md b/workshops/Modeller/index.md index b0249cb..6ecef1e 100644 --- a/workshops/Modeller/index.md +++ b/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.