Science Score: 44.0%
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
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○Academic publication links
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○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 (8.4%) to scientific vocabulary
Keywords
graph-representations
graph-theory
python-package
solvent-accessibility
structural-biology
Last synced: 6 months ago
·
JSON representation
·
Repository
SERD: Solvent-Exposed Residues Detection
Basic Info
- Host: GitHub
- Owner: LBC-LNBio
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Homepage: https://lbc-lnbio.github.io/SERD/
- Size: 170 MB
Statistics
- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 1
- Releases: 0
Topics
graph-representations
graph-theory
python-package
solvent-accessibility
structural-biology
Created over 4 years ago
· Last pushed about 1 year ago
Metadata Files
Readme
License
Citation
README.md
SERD
A Python package to detect solvent-exposed residues of a target biomolecule.
See also:
Installation
To install the latest release on PyPI, run:
bash
pip install SERD
Or to install the latest developmental version, run:
bash
git clone https://github.com/LBC-LNBio/SERD.git
pip install -e SERD
Citation
If you use SERD package, please cite:
Guerra, J. V. S., Jara, G. E., Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2022). SERD (Version v0.1.2) [Computer software]. https://github.com/LBC-LNBio/SERD.
License
The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Owner
- Name: Computational Biology Laboratory - LBC/LNBio/CNPEM
- Login: LBC-LNBio
- Kind: organization
- Email: lbc@lnbio.cnpem.br
- Location: Rua Giuseppe Máximo Scolfaro, 10.000 Polo II de Alta Tecnologia de Campinas - Campinas/SP, Brasil
- Website: https://lnbio.cnpem.br/thematic-programs/bioinformatics/
- Repositories: 7
- Profile: https://github.com/LBC-LNBio
Repository of Computational Biology Laboratory - LBC
Citation (CITATION.cff)
cff-version: 0.1.2
title: SERD
message: >-
If you use SERD in your research, please cite it as below.
type: software
authors:
- given-names: João Victor
family-names: Guerra
email: joao.guerra@lnbio.cnpem.br
affiliation: >-
Brazilian Center for Research in Energy and Materials
(CNPEM)
orcid: 'https://orcid.org/0000-0002-6800-4425'
- affiliation: >-
Brazilian Center for Research in Energy and Materials
(CNPEM)
given-names: Gabriel Ernesto
family-names: Jara
email: gabriel.jara@lnbio.cnpem.br
- given-names: José Geraldo de Carvalho
family-names: Pereira
email: jose.pereira@lnbio.cnpem.br
affiliation: >-
Brazilian Center for Research in Energy and Materials
(CNPEM)
- given-names: Paulo Sergio
family-names: Lopes-de-Oliveira
email: paulo.oliveira@lnbio.cnpem.br
affiliation: >-
Brazilian Center for Research in Energy and Materials
(CNPEM)
repository-code: 'https://github.com/LBC-LNBio/SERD'
url: 'https://lbc-lnbio.github.io/SERD/'
abstract: >-
SERD is a Python package designed to identify
solvent-exposed residues within a target biomolecule,
making them accessible to potential ligands. Furthermore,
SERD has the capability to depict biomolecular
structures as graphs, encompassing various entities,
including binding sites (e.g., cavities identified by
the KVFinder suite) and biomolecular complexes (e.g.,
IPPs, IPLs, IPRs, and IPDs), taking into account their
intramolecular interactions.
keywords:
- structural-biology
- solvent-accessibility
- python-package
- graph-theory
- graph-representations
license: GNU General Public License v3.0
commit: e9ef6e1
version: v0.1.2
date-released: '2022-10-19'
GitHub Events
Total
- Issues event: 1
- Watch event: 1
- Issue comment event: 3
- Push event: 10
- Pull request event: 2
- Create event: 2
Last Year
- Issues event: 1
- Watch event: 1
- Issue comment event: 3
- Push event: 10
- Pull request event: 2
- Create event: 2
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| jvsguerra | j****a@g****m | 76 |
| gabrieliacc | g****r@g****m | 4 |
| gabriel.jara | g****a@l****r | 1 |
| zgcarvalho | z****o@o****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: about 6 hours
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 1.0
- Average comments per pull request: 0.67
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 17 hours
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 2.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jvsguerra (2)
Pull Request Authors
- jvsguerra (2)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels
enhancement (2)
Dependencies
requirements.txt
pypi
- networkx >=2.8.6
- numpy >=1.23.2
- pyKVFinder >=0.4.2
- scipy >=1.9.0
.github/workflows/publish-release.yml
actions
- RalfG/python-wheels-manylinux-build v0.5.0-manylinux2014_x86_64 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
setup.py
pypi