AdK transitions datasets

The MDAnalysisData.adk_transitions module contains ensembles of trajectories during which the close-to-open transiton of the enzyme adenylate kinase [Seyler2014] is sampled using different computational methods [Seyler2015].

fetch_adk_transitions_DIMS([data_home, …])

Load the AdK DIMS transititions dataset

fetch_adk_transitions_FRODA([data_home, …])

Load the AdK FRODA transititions dataset

See also

This set of trajectories was used in the SPIDAL Tutorial: MDAnalysis with Midas/radical.pilot where the ensemble of 400 DIMS+FRODA trajectories is analyzed with the Path Similarity Analysis method [Seyler2015]. Computations on such a large(ish) dataset are sped up by parallelization at the task level with RADICAL-Pilot.

AdK DIMS transitions ensemble dataset

The macromolecular conformational transition between the closed conformation of apo-adenylate kinase from E. coli (EcAdK) to the open conformation was sampled with two methods: (1) dynamic importance sampling molecular dynamics (DIMS MD) [Perilla2009], and (2) Framework Rigidity Optimized Dynamics Algorithm (FRODA) [Farrell2010]. Each ensemble of independently generated paths contains 200 trajectories in the CHARMM DCD format.

This data set contains the DIMS ensemble.

DIMS AdK (implicit solvent) with dynamic importance sampling MD from closed (1AKE) to open (4AKE). CHARMM 22 force field. Topology file: adk4ake.psf

Notes

Data set characteristics:

size

757 MB

number of trajectories

200

number of frames

varies

number of atoms

3341

creator

Sean L. Seyler

URL

https://doi.org/10.6084/m9.figshare.7165306.v2

license

CC-BY 4.0

reference

[Seyler2015]

[Seyler2015] Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path

Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568

MDAnalysisData.adk_transitions.fetch_adk_transitions_DIMS(data_home=None, download_if_missing=True)[source]

Load the AdK DIMS transititions dataset

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>/adk_transitions_DIMS.

  • 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.trajectories (list) – list with filenames of the trajectory ensemble

  • dataset.N_trajectories (int) – number of trajectories in the ensemble

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

See AdK DIMS transitions ensemble dataset for description.

AdK FRODA transitions ensemble dataset

The macromolecular conformational transition between the closed conformation of apo-adenylate kinase from E. coli (EcAdK) to the open conformation was sampled with two methods: (1) dynamic importance sampling molecular dynamics (DIMS MD) [Perilla2009], and (2) Framework Rigidity Optimized Dynamics Algorithm (FRODA) [Farrell2010]. Each ensemble of independently generated paths contains 200 trajectories in the CHARMM DCD format.

This data set contains the FRODA ensemble.

FRODA AdK with geometric targeting on a rigid decomposition (FRODA server); closed (1AKE) to open (4AKE). Topology file: 1ake.pdb (without hydrogens)

Notes

Data set characteristics:

size

539 MB

number of trajectories

200

number of frames

varies

number of atoms

1656

creator

Avishek Kumar

URL

https://doi.org/10.6084/m9.figshare.7165306.v2

license

CC-BY 4.0

reference

[Seyler2015]

[Seyler2015] Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path

Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. https://doi.org/10.1371/journal.pcbi.1004568

MDAnalysisData.adk_transitions.fetch_adk_transitions_FRODA(data_home=None, download_if_missing=True)[source]

Load the AdK FRODA transititions dataset

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>/adk_transitions_FRODA.

  • 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.trajectories (list) – list with filenames of the trajectory ensemble

  • dataset.N_trajectories (int) – number of trajectories in the ensemble

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

See AdK FRODA transitions ensemble dataset for description.

References

Perilla2009(1,2)

J. R. Perilla, O. Beckstein, E. J. Denning, and T. Woolf. Computing ensembles of transitions from stable states: Dynamic importance sampling. 32(2):186–209, 2011.

Farrell2010(1,2)

D. W. Farrell, K. Speranskiy, and M. F. Thorpe. Generating stereochemically acceptable protein pathways. Proteins, 78(14):2908–21, Nov 2010.

Seyler2014

S. L. Seyler and O. Beckstein. Sampling of large conformational transitions: Adenylate kinase as a testing ground. Molec. Simul., 40(10–11):855–877, 2014.

Seyler2015(1,2,3,4)

Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways. PLoS Comput Biol 11(10): e1004568. doi: 10.1371/journal.pcbi.1004568