Data · dataset · 2015
AKeco Structure Library
Listed in Zenodo
The AKecoLib contains 46 models of E. coli adenylate kinase structures that were used to compare a computational approach to simulating macromolecular transitions (dynamic importance sampling) to experimentally observed structures. 1 The structures cover all conformations of AdK, from closed to open.
Description
The structures in the library were generated by homology modelling 2 of the AKeco sequence on AdK structures found in the protein data bank (only variants with the LID domain were considered).
For further details please refer to the paper. 1 When using these structures in your own published work please cite Beckstein et al 1 . See also becksteinlab.physics.asu.edu/resources/73/akeco-structure-library License Copyright © 2009 Oliver Beckstein, Elizabeth J. Denning, Thomas B. Woolf. The structures are made available under a CreativeCommons Attributions-ShareAlike licence 3.0 basically you can modify and share the files but you must attribute them to us (e.g., by citing our paper) and you must make the modified files available under the same or a compatible licence.) "AKeco Structure Library" by O. Beckstein, E. J. Denning, and T. B. Woolf is licensed under a Creative Commons Attribution-ShareAlike 3.0 International License.
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Based on a work at becksteinlab.physics.asu.edu/file_download/16/AKecoLib.tar.bz2. Data Download the file AKecoLib.tar.bz2 und unpack the compressed archive with tar -jxvf AKecoLib.tar.bz2. The directory AKecoLib contains files in the PDB format as written by MODELLER 2 .
The filename (e.g. AKeco_2RH5_A.pdb) indicates (1) the PDB code of the template and (2) the chain in the template (e.g. chain A of PDB: 2RH5). References a b c O. Beckstein, E. J. Denning, J. R. Perilla, and T. B. Woolf. Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open / closed transitions .
J. Mol. Biol., 394(1):160–176, 2009. a b N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER.
Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
Links
Get the data
- AKecoLib.tar.bz2 zenodo.org/api/records/29243/files/AKecoLib.tar.bz2/content ↗
download · from Zenodo
Where it is published
- Zenodo record zenodo.org/records/29243 ↗
landing page · from Zenodo
- DOI doi.org/10.5281/zenodo.29243 ↗
DOI / persistent id · from Zenodo
Documentation and papers
- IsSupplementTo 10.1016/j.jmb.2009.09.009 doi.org/10.1016/j.jmb.2009.09.009 ↗
publication · from Zenodo
Catalogue records · 1
- Zenodo API zenodo.org/api/records/29243 ↗
metadata API · from Zenodo
Topics
- Inferred from text
- Structural biology 76%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Zenodo | 29243 | 15 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · Zenodo | connector:zenodo@1.0.0 | /metadata/access_right |
| byte_size | source · Zenodo | connector:zenodo@1.0.0 | |
| concepts[field].anzsrc:field:310112 | enrichment · Zenodo | taxonomy-embedding@1.1.0 | title+keywords+description (76%) |
| created_date | source · Zenodo | connector:zenodo@1.0.0 | |
| description | source · Zenodo | connector:zenodo@1.0.0 | /metadata/description |
| license | source · Zenodo | connector:zenodo@1.0.0 | /metadata/license |
| publication_date | source · Zenodo | connector:zenodo@1.0.0 | |
| title | source · Zenodo | connector:zenodo@1.0.0 | /metadata/title |
| updated_date | source · Zenodo | connector:zenodo@1.0.0 |