Data · dataset · 2025
Hb Molecular Dynamics
Listed in ScienceDB
Included within this repository are all protein models (.pdb) used for molecular dynamics studies of methemoglobin from different agriculturally relevant species (i.e. trout and cattle).
Description
Also included are all simulation trajectory (.xtc) files for all replicates. Models and their corresponding trajectory files can be visualized in common molecular visualization software (e.g. PyMol, Chimera).
Each folder is named according to its contents. Within each folder is the model and trajectory files of all simulation replicates performed. The corresponding article has been submitted to the ACS Journal of Agriculture and Food Chemistry.All models were generated from previously published crystal structures in CHARMM GUI, and output files were generated suing GROMACS molecular dynamics software.
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Each replicate was trajectory was produced using random velocity generation.File size:Models files (.pdb) = ~8 MBTrajectory files (.xtc) = 200-500 MB
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.19468 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Biochemistry and cell biology 74% · Simulation 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.19468 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3101 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (74%) |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[method].local:method:simulation | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |