Here is the raw data and supplementary materials related to our recent CAP research. Related papers:
Pangenome analysis of Ca2+-ATPases in rhododendrons offers insights into distinct evolution, expression and conformational motion
Files:
Structures.7z #Raw data file for CAPs three-dimensional structures.
Conformation_motion_prediction_(based_on_AFF2024).7z
│ │ #Conformation motion prediction algorithm AFF2024
│ │ (https://github.com/Gxy-with-luv/AFF2024/blob/main/Walkthrough.ipynb)
│ │ based on AlphaFold2. We modified the script to adapt it to CAPs.
│ │ The method used is the HF-site masking from AFF2024.
│ │
│ │
│ ├── MSA.a3m #Sequence alignment file.
│ │
│ ├── natbox.npy #Local energy matrix of Rb02G0001032.
│ │
│ ├── sing.npy #Energy matrix generated by multi-sequence thread on Rb02G0001032.
│ │
│ ├── CAP-HFsites_masking_predict_90.ipynb #Modified HF-site masking methods pipeline.
│ │
│ └── Predicted/ #Predicted results of conformational motion after HF-site masking.
Conformation_motion_prediction_(modified).7z
# Raw results of predicting the conformational motion of three CAP genes through our modified pipeline.
FrustrationData&Rosetta-energy/ # Raw data from Rosetta and Frustratometer calculations.
│ │
│ ├── FrustrationData.7z #The frustration information of CAP proteins in rhododendrons, including
│ │ the density fraction of highly frustrated contacts surrounding the residues.
│ │ *configurational_5adens can be viewed using Excel.
│ │
│ ├── FrustrationVisualization.7z #Visualization files for the frustration networks of the local
│ │ energy of CAPs in protein structures. The visualization of
│ │ frustration networks can be achieved by inputting the *.pml file
│ │ into Pymol.
│ │
│ │
│ ├── Rosetta-energy.7z #Raw file for Rosetta energy calculations.
│ │
│ ├── *.xml # Auxiliary files for Rosetta scripts to calculate protein energy.
│ │
│ └── *.log # Rosetta scripts calculation results file for protein energy.
│ *.log can be viewed using Excel.