TAS2R_data

Code and data for the TAS2R paper:

Functional Molecular Switches of Mammalian G Protein-Coupled Bitter-Taste Receptors
Jérémie Topin †*, Cédric Bouysset †, Jody Pacalon, Yiseul Kim, MeeRa Rhyu, Sébastien Fiorucci *, Jérôme Golebiowski

Description

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• mammalian-TAS2R.pir: MSA of mammalian TAS2R sequences
• TAS2R-OR-templates.pir: MSA used to generate the homology models
• TAS2R-msa-annotated.xlsx: Excel spreadsheet containing the annotated sequence
• The 3D models directory contains the PDB files for each of the 25 human TAS2R models with the highest meta-score. The tempfactor inside the PDB file has been modified to correspond to the sequence identity between TAS2Rs.
• The scripts directory contains the code that was used in the current paper:
  • 01-generate-models.py: Modeller script used to generate 3D models of TAS2Rs
  • 02-analysis.ipynb: Analysis notebook to score all models
  • pocket.pdb: Set of points used to generate the binding pocket of the receptor used for scoring
  • msa.xlsx: Simplified version of the TAS2R-msa-annotated.xlsx file
  • all_scores_models_final.pkl: The complete table of scores for each receptor, protocol and template, excluding missfolded models. Can be read directly in pandas with pd.read_pickle("all_scores_models_final.pkl")

Requirements

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mdanalysis=1.0.0
modeller=9.21
numpy=1.19.0
pandas=1.0.1
scipy=1.5.0