Data · dataset · 2025
Molecular Dynamics Simulation Data of FAT10
Listed in RADAR and RADAR4Memory — shown once because both records carry DOI 10.48606/gx4q9ureeuzxsndv
This data set contains molecular dynamics simulations of the ubiquitin-like signaling protein FAT10 (Ubiquitin-D).
Description
It is composed of 150 simulation trajectories with 200 ns simulated time and a time interval between frames of of 100ps. The dataset contains three replicates of 50 different simulation conditions - 2 different ion concentrations and 25 different starting conformations.
The ion conditions are "no NaCl" and "150 mM NaCl". The starting conformations were generated by rotating the Phi-angle of residue Asp85 by 360° in 25 steps. This angle in the flexible linker of FAT10 modifies the relative orientation of its two ubiquitin-like domains.
Read the rest (2 more)
The simulations were performed using the GROMACS simulation package version 2018, 2020 and 2021 and the GROMOS96 54/A7 force field. This dataset accompanies a publication which proposes a clustering framework for the applying of network formalisms to flexible protein systems (analysis code available under: github.com/AG-Peter/Clustering_Networks, publication available under: doi.org/10.1021/acs.jcim.5c01298 ).
Please cite this work if you are using the dataset in a publication.
Links
Where it is published
- DOI doi.org/10.48606/gx4q9ureeuzxsndv ↗
DOI / persistent id · from radar service eu de
Catalogue records · 1
- OAI-PMH record radar-service.eu/oai/OAIHandler?verb=GetRecord&metadataPrefix=oai_dc&identifier… ↗
metadata API · from radar service eu de
Topics
- From keywords
- Chemistry · Chemistry · Earth & Environmental Science · Earth & Environmental Science · Life Sciences · Life Sciences
- Inferred from text
- Biochemistry and cell biology 73% · Simulation 75%
Provenance · 2 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| RADAR | 10.48606/gx4q9ureeuzxsndv | 12 d ago | JSON v1 |
| RADAR4Memory | 10.48606/gx4q9ureeuzxsndv | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · radar service eu de | connector:radar_service_eu_de@1.0.0 | |
| concepts[field].anzsrc:group:3101 | enrichment · radar service eu de | taxonomy-embedding@1.1.0 | title+keywords+description (73%) |
| concepts[field].local:field:chemistry | mapping · radar service eu de | connector:radar_service_eu_de@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · radar4memory radar service eu | connector:radar4memory_radar_service_eu@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · radar service eu de | connector:radar_service_eu_de@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · radar4memory radar service eu | connector:radar4memory_radar_service_eu@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · radar4memory radar service eu | connector:radar4memory_radar_service_eu@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · radar service eu de | connector:radar_service_eu_de@1.0.0 | |
| concepts[method].local:method:simulation | enrichment · radar service eu de | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · radar service eu de | connector:radar_service_eu_de@1.0.0 | /metadata/dc/description |
| license | source · radar service eu de | connector:radar_service_eu_de@1.0.0 | /metadata/dc/rights |
| publication_date | source · radar service eu de | connector:radar_service_eu_de@1.0.0 | |
| title | source · radar service eu de | connector:radar_service_eu_de@1.0.0 | /metadata/dc/title |