Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
(2024)
- Author
- Jose Gavalda-Garcia and Bhawna Dixit (UGent)
- Organization
- Abstract
- This data set contains the three data sets for the article, "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics." In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below. 1. S2RCI data set: Chemical-shift based estimates of dynamics and conformation (S2RCI, δ2D, ShiftCrypt). 2.S2 data set: Experimentally measured order parameter from NMR relaxation data. 3. MD data set (Constava): For Conformational state variability and propensities, calculated with the Constava software from Molecular Dynamics trajectories [(go to Python package on PyPI)](https://pypi.org/project/constava/). The S2RCI and MD datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: AlphaFold2 Models: Both original and truncated structures. WEBnma Modes: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. Root-Mean-Square-Fluctuations (RMSF): Profiles calculated before and after truncation of AF2 models. NMR Data: Normal Mode Analysis (NMA): Performed on corresponding NMR ensembles (see below). The NMR Data of NMA in these datasets includes: NMR ensembles Individual NMR models extracted from each ensemble STRIDE secondary structure calculations per-individual NMR models RMSF profiles per-individual NMR models For detailed information, please refer to the `Readme.txt` file within each corresponding folder. The S2 dataset includes all the features listed above, except for the NMR analysis.
- License
- CC-BY-4.0
- Access
- open access
Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01JD71GARCK4XFEV2BG44KZBHY
@misc{01JD71GARCK4XFEV2BG44KZBHY,
abstract = {{This data set contains the three data sets for the article, "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics."
In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.
1. S2RCI data set: Chemical-shift based estimates of dynamics and conformation
(S2RCI, δ2D, ShiftCrypt).
2.S2 data set: Experimentally measured order parameter from NMR relaxation data.
3. MD data set (Constava): For Conformational state variability and propensities,
calculated with the Constava software from Molecular Dynamics trajectories [(go to Python package on PyPI)](https://pypi.org/project/constava/).
The S2RCI and MD datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature:
AlphaFold2 Models: Both original and truncated structures.
WEBnma Modes: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models.
Root-Mean-Square-Fluctuations (RMSF): Profiles calculated before and after truncation of AF2 models.
NMR Data: Normal Mode Analysis (NMA): Performed on corresponding NMR ensembles (see below).
The NMR Data of NMA in these datasets includes:
NMR ensembles
Individual NMR models extracted from each ensemble
STRIDE secondary structure calculations per-individual NMR models
RMSF profiles per-individual NMR models
For detailed information, please refer to the `Readme.txt` file within each corresponding folder.
The S2 dataset includes all the features listed above, except for the NMR analysis.}},
author = {{Gavalda-Garcia, Jose and Dixit, Bhawna}},
language = {{eng}},
publisher = {{Zenodo}},
title = {{Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"}},
url = {{http://doi.org/10.5281/zenodo.10977724}},
year = {{2024}},
}
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