coevo_dimer

CBMFW4761 at Columbia University, SP22 Group project title: investigating the Implications of coevolution in heterodimeric protein complexes

• Dylan Marshall, Columbia Systems Biology PhD student
• Julia Urban, Columbia Systems Biology PhD student
• Peiwen Cai, Columbia Systems Biology PhD student

4 heterodimers from Ovchinnikov et al 2014, eLife are included. Under each __dimer_name__ folder, the followings are included:

• AF2.ipynb: modified based on ColabFold for structural prediction of the heterodimer
• msa.pickle: paired MSA from AF2 above
• rank_1_model_1_ptm_seed_0_relaxed.pdb: PDB file
• MRF_analysis.ipynb: MRF model
• *_coevo.pickle: coevolutionary coefficient matrcies from MRF_analysis.ipynb

results_merged.ipynb provides code for data analysis (e.g. MSA bootstrapping) and visualizations. all jupyter notebooks are run on Google-Colab GPU; all package dependency requirements are addressed in corresponding notebooks.