https://github.com/kull-centre/ensemblelab
Science Score: 21.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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✓Institutional organization owner
Organization kull-centre has institutional domain (www1.bio.ku.dk) -
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○Scientific vocabulary similarity
Low similarity (5.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: KULL-Centre
- License: gpl-3.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 93.8 KB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
EnsembleLab
Google Colaboratory-based notebooks to study conformational ensembles of proteins.
IDRLab
MD simulations of IDPs and IDRs with the CALVADOS2 coarse-grained model, including calculation of sequence features and structural parameters.
Run the notebook on Google Colab.
If you use IDRLab, we ask you to cite Tesei, Trolle et al. [1]. In addition, you may consider citing Tesei & Lindorff-Larsen [2] for CALVADOS 2 and Eastman et al. [3] for OpenMM.
[1] G. Tesei, A. I. Trolle, N. Jonsson, J. Betz, F. Pesce, K. E. Johansson, K. Lindorff-Larsen Conformational ensembles of the human intrinsically disordered proteome: Bridging chain compaction with function and sequence conservation bioRxiv 2023 2023.05.08.539815 DOI: https://doi.org/10.1101/2023.05.08.539815
[2] G. Tesei and K. Lindorff-Larsen Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range [version 2; peer review: 2 approved] Open Research Europe 2023 2(94) DOI: https://doi.org/10.12688/openreseurope.14967.2
[3] P. Eastman, J. Swails, J. D. Chodera et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics PLoS Computational Biology 2017 13(7):e1005659 DOI: https://doi.org/10.1371/journal.pcbi.1005659
Owner
- Name: Linderstrøm-Lang Centre for Protein Science, University of Copenhagen
- Login: KULL-Centre
- Kind: organization
- Location: Copenhagen, Denmark
- Website: https://www1.bio.ku.dk/english/research/bms/research/llc/
- Repositories: 8
- Profile: https://github.com/KULL-Centre