Supplementary data for the paper "Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors"
- Type of resource
- software, multimedia
- Date created
- June 2017
It is unclear how the known atomic structures of NMDA receptors (NMDARs) relate to the functional states of NMDARs inferred from electrophysiological recordings. We address this problem by all-atom computer simulations, a method successfully applied in the past to much smaller biomolecules. Our simulations predict that four ‘non-active’ cryoEM structures of NMDARs rapidly interconvert on submicrosecond timescales, and therefore, correspond to the same functional state of the receptor.
The files 'structures_and_computations.zip' and 'structures_and_computations.tar.gz' (the same contents, different archiving formats) contain scripts and high-level data mentioned in the paper (computation of time-independent based components, specification of Markov state models, etc.). The file 'trajectories.tar' can be assembled from the provided 280 files named 'trajectories.tar.part_*' by "cat trajectories.tar.part_* > trajectories.tar". The file 'trajectories.tar' contains the molecular dynamics trajectories of NMDA receptors used in this paper. Note that 'trajectories.tar' is 2.8 Tb in size, as well as the folder generated by untarring it.
- Related Publication
- Sinitskiy, A.V. and Pande, V.S. (2018). Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors. Biophysical Journal. https://doi.org/10.1016/j.bpj.2018.06.023
- Preferred Citation
- Sinitskiy, Anton and Pande, Vijay. (2017). Supplementary data for the paper "Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors." Stanford Digital Repository. Available at: http://purl.stanford.edu/jf301dx7536
- Stanford University. Libraries
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