Table 1 Hierarchical organization of the data fields in the mdCATH dataset, with units and description.
From: mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics
Field | Size | Type | Unit | Description |
|---|---|---|---|---|
Domain ID/ | ||||
chain | N | string | Chain ID | |
element | N | string | Chemical element | |
pdb | 1 | string | PDB file used for simulation | |
psf | 1 | string | Topology file used for simulation | |
pdbProteinAtoms | 1 | string | PDB file with the N reported atoms | |
resid | N | integer | Residue number | |
resname | N | string | Residue name | |
z | N | integer | Atomic number | |
.numResidues | 1 | integer | Number of residues (attribute) | |
320/ | Group for the 320 K simulations | |||
0/ | Data of the first replica | |||
coords | F × N × 3 | float | Å | Atom coordinates |
forces | F × N × 3 | float | kcal/mol/Å | Forces |
dssp | F × R | string | DSSP secondary str. assignments | |
gyrationRadius | F | double | nm | Gyration radius |
rmsd | F | float | nm | Root-mean square deviation w.r.t. begin |
rmsf | R | float | nm | Cα root-mean-square fluctuation |
box | 3 × 3 | float | nm | Simulation unit cell |
.numFrames | 1 | integer | Number of frames for this replica (attribute) | |
1/ | Second replica | |||
… | ||||
348/ | ||||
… | ||||
