Supplementary Data for "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29" by Szadkowska M, Kocot AM, Sowik D, Wyrzykowski D, Jankowska E, Kozlowski LP, Makowska J, Plotka M

Bioinformatics results related to the article "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29"Sequence:>AYJ74695.1 lysozyme [Thermus phage phiKo]MNWIEFWRSKKPTWRHRPVDPAYIVLHHTAGPVDQAPQAIWDYHVKVRGWPHGGYHFLVYHDGTVVKMLPLSAQPICVGEYNHLAICIALVGNFVGGYPPEWNERAPGWKSLAWLVRELRKHDSGLRLRLVRHKDLRPTKCPGTVTWEEALVRGGVPQEQVETLKVAGVIA>RAP-29 - phiKo derived potent antimicrobial peptide (105-133 aa)RAPGWKSLAWLVRELRKHDSGLRLRLVRHModels are done by:1) Phyre2 (intensive mode) ./models/phyre2/final.casp.pdb2) hhsearch+modeller (modelled on all templates) - quite poor model ./models/modeller_2483784.pdb3) AlphaFold2 (colab over pdb70) ./models/PhiKo_f9d15.result.af24) deepfold (https://zhanggroup.org/DeepFold/) - quite poor model ./models/DeepFold/model1_DeepFold.pdb5) omegafold./models/omegafold/phiKo.pdb6) RGN2 - unexpectly, quite poor model./models/RGN2/phiKo_729bd0_prediction_RGN2.pdb7) RoseTTAFold (run online)./models/rosseta8) ESMFold --> the best model./models/ESMFold/ptm0.912_r3_default.ESMFold.pdbAdditionally, from one of the templates (Ts2631 PDB:6SU5) Zn i PO4 had been taken to complement the catalytic center.├── figure1_alignment.gb├── models│  ├── all_models_aligned.pdf│  ├── all_models_aligned.tif│  ├── all_models_aligned_Zn_added.py│  ├── all_models_aligned_Zn_added.pyc│  ├── DeepFold│  ├── ESMFold│  ├── Fig_S1a.png│  ├── Fig_S1a_ray.png│  ├── Fig_S1b.png│  ├── Fig_S1b_ray.png│  ├── Fig_S1.png│  ├── Fig_S2a.png│  ├── Fig_S2.png│  ├── modeller_2483784.pdb│  ├── model_with_black105-133.tif│  ├── model_with_black140.tif│  ├── omegafold│  ├── phiKo_all.mp4│  ├── phiKo_catalitic_center_closeup_T7_Ts2631.py│  ├── phiKo_catalitic_center_plus_K140.py│  ├── phiKo_catalitic_center_plus_K140.pyc│  ├── phiKo_catalitic_center.py│  ├── phiKo_catalytic_center_all.mp4│  ├── phiKo_catalytic_center_all.pdf│  ├── phiKo_catalytic_center_all.tif│  ├── phiKo_catalytic_center_plus_K140.webm│  ├── phiKo_catalytic_center.tif│  ├── PhiKo_f9d15.result.af2│  ├── phiKo_main_model_with_ligands_all_models.py│  ├── phiKo_main_model_with_ligands_all_models.pyc│  ├── phiKo_main_model_with_ligands_all_models_v2.py│  ├── phiKo_main_model_with_ligands.pdb│  ├── phiKo_main_model_with_ligands.py│  ├── phiKo_main_model_with_ligands.tif│  ├── phiKo.mp4│  ├── phiKo_vs_T7.mp4│  ├── phiKo_vs_T7.pdf│  ├── phiKo_vs_T7.py│  ├── phiKo_vs_T7.pyc│  ├── phiKo_vs_T7.tif│  ├── phiKo_vs_T7_Ts2631_ph2119.png│  ├── phiKo_vs_T7_Ts2631_ph2119.py│  ├── phiKo_vs_Ts2631.mp4│  ├── phiKo_vs_Ts2631.py│  ├── phiKo_vs_Ts2631.pyc│  ├── phiKo_vs_Ts2631.tif│  ├── phyre2│  ├── RGN2│  └── rosseta├── phiKo.fas├── RAP-29.fas└── README.txtFiles *.py are UCSF Chimera viewer sessions storing superposition of multiple models, homolog proteins, catalytic center zoom in, etc.