Databank structure

All data of the databank lives in the Data folder of the repository:

Data/
├── info_files/      input files for AddData.py, one folder per simulation
├── Simulations/     one folder per simulation, addressed by file hashes
├── Experiments/     experimental data, one folder per experiment type
└── Molecules/       molecule definitions and mapping files

Input files (Data/info_files)

Each simulation is added with an info.yaml file that names the raw data and describes the system. A minimal example:

DOI: 10.5281/zenodo.15393821
SOFTWARE: gromacs
TRJ: replica_01_AMBER03WS_md_1500ns.xtc
TPR: replica_01_AMBER03WS_md_1500ns.tpr
PREEQTIME: 0
TIMELEFTOUT: 0

COMPOSITION:
  PROTEIN:
  SOL:
    NAME: SOL
    MAPPING: mappingTIP4PSwater.yaml
  CLA:
    NAME: CL
    MAPPING: mappingCLAecc.yaml

DIR_WRK: /tmp/tmpData/
PUBLICATION: https://doi.org/...
AUTHORS_CONTACT: Name
SYSTEM: ChiZ1-64
FF: AMBER03WS

DOI points to the repository (typically Zenodo) that holds the trajectory TRJ and topology TPR. COMPOSITION lists the molecules in the system by their universal names; the PROTEIN entry is filled in by AddData.py with the sequence extracted from the topology, and the other entries refer to mapping files in Data/Molecules.

Simulations (Data/Simulations)

Simulation folders are addressed by the SHA1 hashes of the trajectory and topology files, split into a directory tree, e.g. Data/Simulations/8e2/c75/8e2c75ee.../5e0ddfac.../. Each folder contains the README.yaml written by AddData.py and the properties computed by the analysis scripts:

README.yaml

The metadata of the simulation. Besides the fields copied from info.yaml it contains ID, TYPEOFSYSTEM (protein), TEMPERATURE, NUMBER_OF_ATOMS, TRAJECTORY_SIZE, TRJLENGTH, DATEOFRUNNING, the COMPOSITION with molecule counts and the PROTEIN sequence, and the EXPERIMENT block listing the matched chemical_shift, saxs and spin_relaxation experiments together with their alignment score and condition matches.

Contact_map.png, Distance_map.png

Residue-residue contact probabilities and distances.

Backbone_correlations.csv, Backbone_correlations.png

Backbone N-H correlation functions.

dynamic_landscape_Coeffs.yaml

Coefficients of the dynamic landscape fit.

spin_relaxation_times.yaml

Computed NMR spin relaxation times.

gyrate.xvg

Radius of gyration along the trajectory.

SAXS.yaml

Computed SAXS profile.

chemical_shifts_sparta.yaml, chemical_shift_rmsd.yaml, chemical_shift_quality.yaml

Computed chemical shifts and their comparison to experiments.

secondary_structure.yaml

Secondary structure populations.

Experiments (Data/Experiments)

Experiments are grouped by type, saxs, chemical_shift and spin_relaxation, and then by the DOI or database ID of the publication:

Data/Experiments/saxs/10.1038/srep30473/
├── fasta.yaml            protein sequence(s)
└── saxs_metadata.yaml    sample components and conditions

fasta.yaml holds the sequence used for alignment against the simulated protein. The metadata file lists the sample components with their concentrations (protein, buffer, salt) and the sample conditions (pH, temperature), which searchDatabank.py uses to decide whether an experiment matches a simulation. Chemical shift and spin relaxation experiments are retrieved from the BMRB with create_experimental_data_file.py and additionally contain the measured data, e.g. spin_relaxation_times.yaml.

Molecules (Data/Molecules)

Molecule definitions and mapping files are organised in membrane, protein and solution. A mapping file connects the simulation specific atom names of a molecule to the universal names used by the analysis code, exactly as in the lipid databank.