I-FABP dataset

The MDAnalysisData.ifabp_water module contains a short equilibrium MD trajectory of the globular protein intestinal fatty acid binding protein (I-FABP) with all the solvent included (water and ions). It can be used to study protein dynamics, protein-ion, and protein-water interactions.

fetch_ifabp_water([data_home, ...])

Load the I-FABP with water 0.5 ns equilibrium trajectory

I-FABP in water dataset

The trajectory is a short MD run of I-FABP (intestinal fatty acid binding protein) in water.

It was simulated in CHARMM for 500 ps with a 2 fs timestep. Frames were saved every 1 ps and the trajectory was RMSD-fitted to the protein.

There are 500 frames in the trajectory.

It is used as a test case for the hop package.

Notes

Data set characteristics:

size:

74 MB

number of trajectories:

1

number of frames:

500

number of particles:

12445

creator:

Oliver Beckstein

URL:

10.6084/m9.figshare.7058030.v1

license:

CC-BY 4.0

reference:

[Beckstein2018]

[Beckstein2018]

Beckstein, Oliver (2018): Molecular dynamics trajectory of I-FABP for testing and benchmarking solvent dynamics analysis. figshare. Fileset. DOI: 10.6084/m9.figshare.7058030.v1

MDAnalysisData.ifabp_water.fetch_ifabp_water(data_home=None, download_if_missing=True)[source]

Load the I-FABP with water 0.5 ns equilibrium trajectory

Parameters:

  • data_home (optional, default: None) – Specify another download and cache folder for the datasets. By default all MDAnalysisData data is stored in ‘~/MDAnalysis_data’ subfolders. This dataset is stored in <data_home>/ifabp_water.

  • download_if_missing (optional, default=True) – If False, raise a IOError if the data is not locally available instead of trying to download the data from the source site.

Returns:

  • dataset (dict-like object with the following attributes:)

  • dataset.topology (filename) – Filename of the topology file

  • dataset.trajectory (filename) – Filename of the trajectory file

  • dataset.structure (filename) – Filename of a structure file in PDB format

  • dataset.DESCR (string) – Description of the trajectory.

See I-FABP in water dataset for description.