geometricus
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 12 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.5%) to scientific vocabulary
Keywords
Repository
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
Basic Info
- Host: GitHub
- Owner: TurtleTools
- License: mit
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: https://turtletools.github.io/geometricus/
- Size: 12.9 MB
Statistics
- Stars: 37
- Watchers: 4
- Forks: 11
- Open Issues: 6
- Releases: 4
Topics
Metadata Files
README.md
Geometricus Represents Protein Structures as Shape-mers derived from Moment Invariants
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
See the documentation.
Installation
Geometricus is a Python (3.9+) package with NumPy, SciPy, Numba, PyTorch and ProDy as dependencies.
Install with pip install git+https://github.com/TurtleTools/geometricus.git
Usage
See the Getting Started page for example usage.
Publications
Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D J van Dijk, Geometricus represents protein structures as shape-mers derived from moment invariants, Bioinformatics, Volume 36, Issue Supplement_2, December 2020, Pages i718–i725, https://doi.org/10.1093/bioinformatics/btaa839
Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D.J. van Dijk, Fast and adaptive protein structure representations for machine learning, bioRxiv 2021.04.07.438777; doi: https://doi.org/10.1101/2021.04.07.438777
Mehmet Akdel, Douglas E V Pires, Eduard Porta Pardo, Jürgen Jänes, Arthur O Zalevsky, Bálint Mészáros, Patrick Bryant, Lydia L. Good, Roman A Laskowski, Gabriele Pozzati, Aditi Shenoy, Wensi Zhu, Petras Kundrotas, Victoria Ruiz Serra, Carlos H M Rodrigues, Alistair S Dunham, David Burke, Neera Borkakoti, Sameer Velankar, Adam Frost, Kresten Lindorff-Larsen, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David B Ascher, Janet M Thornton, Norman E Davey, Amelie Stein, Arne Elofsson, Tristan I Croll, Pedro Beltrao, A structural biology community assessment of AlphaFold 2 applications, bioRxiv 2021.09.26.461876; doi: https://doi.org/10.1101/2021.09.26.461876
Janani Durairaj, Joana Pereira, Mehmet Akdel, Torsten Schwede, What is hidden in the darkness? Characterization of AlphaFold structural space, bioRxiv 2022.10.11.511548; doi: https://doi.org/10.1101/2022.10.11.511548
Owner
- Name: TurtleTools
- Login: TurtleTools
- Kind: organization
- Repositories: 4
- Profile: https://github.com/TurtleTools
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Durairaj" given-names: "Janani" - family-names: "Akdel" given-names: "Mehmet" - family-names: "Ridder" given-names: "Dick" name-particle: "de" - family-names: "Dijk" given-names: "Aalt D J" name-particle: "van" title: "Geometricus represents protein structures as shape-mers derived from moment invariants" doi: 10.1093/BIOINFORMATICS/BTAA839 version: 0.2.0 date-released: 2020-12-29 identifiers: - type: doi value: 10.1093/BIOINFORMATICS/BTAA839 - type: other value: urn:issn:1367-4803 - type: other value: pmid:33381814 url: "https://github.com/TurtleTools/geometricus"
GitHub Events
Total
- Issues event: 1
- Watch event: 4
- Issue comment event: 3
- Fork event: 4
Last Year
- Issues event: 1
- Watch event: 4
- Issue comment event: 3
- Fork event: 4
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 93
- Total Committers: 8
- Avg Commits per committer: 11.625
- Development Distribution Score (DDS): 0.473
Top Committers
| Name | Commits | |
|---|---|---|
| Ninjani | 4****i@u****m | 49 |
| Ninjani | j****j@g****m | 17 |
| Ninjani | 13 | |
| akdel | m****l@h****m | 7 |
| akdel | a****t@g****m | 3 |
| Terlouw, Barbara | b****w@w****l | 2 |
| Durairaj, Janani | j****j@w****l | 1 |
| biridir | b****r@p****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 10
- Total pull requests: 18
- Average time to close issues: 4 months
- Average time to close pull requests: 8 days
- Total issue authors: 3
- Total pull request authors: 4
- Average comments per issue: 0.2
- Average comments per pull request: 0.06
- Merged pull requests: 15
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- akdel (5)
- Ninjani (4)
- Max1461 (1)
- xjhzjucas (1)
Pull Request Authors
- Ninjani (11)
- akdel (5)
- dependabot[bot] (1)
- AlejandroSanchezCano (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 25 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 6
- Total maintainers: 1
pypi.org: geometricus
Fast, structure-based, alignment-free protein embedding
- Homepage: https://github.com/TurtleTools/geometricus
- Documentation: https://geometricus.readthedocs.io/
- License: MIT License
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Latest release: 0.3.0
published almost 4 years ago