The data processing for the simulation data of Fab A33
SASA
Non-polar SASA
Sum of APR ΔSASA of the 7 APRs
Native contacts
RMSF
Net charges
Salt bridges
Hydrogen bonds
| Feature | Rationale | Action |
|---|---|---|
| SASA (global) | SASA is a measure of how much of the area of a molecule is available to the solvent. The atomic SASA can be used as a measure of the steric availability of an atom. | Calculate the polar SASA for all the atoms inside one residue and then plus them together to get a final polar SASA at a residue level. GROMACS |
| Non-polar SASA | SASA-NP is the accessible surface area of all non-polar atoms. | GROMACS + index file |
| APR | APR score tells you which residue is most solvent accessible | Comput Struct Biotechnol J. 2021; 19: 2726–2741. Cheng Zhang. |
| Fraction of native contacts | The percentage of the contacts that exist within a native state in every frame | MDanalysis package |
| RMSF | It measures the fluctuation of an atom or e.g., a protein residue along the course of a simulation, and is useful to identify the most mobile regions | GROMACS |
| Net charges | It indicates the net charge of the protein at different pHs | PropKa |
| Salt bridges | It is the average of the salt bridge occurrence in the last 50ns | MDanalysis |
| Hydrogen bonds | It measures the number of hydrogen bonds over time | GROMACS |
python packages
- pandas
- Dtale
- re
- fnmatch
- lazy predict
- seaborn
- matplotlib.pyplot
R packages