FAIRMD IDP Databank
FAIRMD IDP is a preliminary databank of molecular dynamics (MD) simulations of intrinsically disordered proteins (IDPs) developed in the FAIRMD project. It works in the same way as the FAIRMD Lipids databank (formerly NMRlipids Databank): simulations are described by metadata files, analysed with a common set of scripts, and compared against experimental data such as small-angle X-ray scattering (SAXS), NMR chemical shifts and NMR spin relaxation times.
FAIRMD IDP is an overlay databank
Each simulation entry contains a README.yaml file that stores all the
essential information for reusing the data, such as the permanent location of
each trajectory file (a DOI), the force field, the protein sequence and the
simulation conditions. The raw trajectories stay in distributed locations
outside the databank, typically Zenodo. The properties
computed from the trajectories are stored next to the README.yaml file.
The organisation of the Data folder is described in Databank structure.
Python API
The library that backs the scripts is distributed as the fairmd.idp
package. It provides the initialisation of the databank
(fairmd.idp.core), general helpers to access simulation files
(fairmd.idp.databankLibrary, fairmd.idp.databankio) and the
protein specific analyses and quality evaluations
(fairmd.idp.protein_functions). See Getting started for a minimal
example and API reference for the full reference.
Adding simulations and running analyses
Simulations are added with AddData.py from an info.yaml file, and the
properties are computed with calcProperties.py. The available scripts are
described in Databank scripts.
Installation
The package is installed with pip straight from GitHub:
pip install git+https://github.com/ohsOllila/IDPdatabank.git
or, from a clone of the repository, as an editable install:
git clone https://github.com/ohsOllila/IDPdatabank.git
cd IDPdatabank
pip install -e .
The scripts and the library need access to the Data folder of the cloned
repository. Set NMLDB_ROOT_PATH to the cloned folder when the package is
not installed in editable mode from that clone. See Getting started.
Python Interface
IDP Databank
Development