Project Title

Analysis of AlphaFold2 for Modeling Structures of Wildtype and Variant Protein Sequences. Lets check this.

Datafile

• ssym_684.xlsx
• ssym_684_copy.xlsx
• ssym_684_classified.csv

Data generation

• python data_generators/generate_fasta_for_alphafold2.py:
• python data_generators/classify_data.py:

Analysis

• python analyzers/dataset_distribution.py
• python analyzers/compute_global_quality_scores.py
• python analyzers/compute_global_quality_stats.py
• python analyzers/plot_global_quality.py
• python analyzers/compute_local_plddt_scores.py
• python analyzers/compute_local_plddt_stats.py
• python analyzers/plot_local_plddt_conf.py
• python analyzers/compute_mutation_side_chain_analysis_scores.py
• python analyzers/plot_mutation_side_chain_analysis_scores.py
• python analyzers/compute_correlation_rmsd_and_plddt.py

Data issues

• Issue 1: 1briA's 1st residue is VAL which does not report CA atom, in that case consider C atom.

Other software usage

• DSSP for secondary structure comparison.
  • Homepage: https://swift.cmbi.umcn.nl/gv/dssp/
  • Github link and installation guide: https://github.com/PDB-REDO/dssp
• TMscore (Zhang lab) to compute the globabl structure similarities: TM-Score, GDT-TS, GDT-HA and MaxSub-Score.
  • Homepage: https://zhanggroup.org/TM-score/