.. -*- coding: utf-8 -*- .. _adk-transitions: ========================== AdK transitions datasets ========================== .. module:: MDAnalysisData.adk_transitions The :mod:`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]_. .. currentmodule:: MDAnalysisData.adk_transitions .. autosummary:: fetch_adk_transitions_DIMS fetch_adk_transitions_FRODA .. SeeAlso:: 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`_. .. _`SPIDAL Tutorial: MDAnalysis with Midas/radical.pilot`: https://www.mdanalysis.org/SPIDAL-MDAnalysis-Midas-tutorial/ .. _`RADICAL-Pilot`: https://radical-cybertools.github.io/ .. include:: ../MDAnalysisData/descr/adk_transitions_DIMS.rst .. autofunction:: fetch_adk_transitions_DIMS .. include:: ../MDAnalysisData/descr/adk_transitions_FRODA.rst .. autofunction:: fetch_adk_transitions_FRODA .. rubric:: References .. [Perilla2009] 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] 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] 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 `_