https://github.com/concept-lab/shrec22_proteinligandbenchmark
Dataset and evalutaion tools of the Shrec 2022 contest on protein-ligand binding site recognition
https://github.com/concept-lab/shrec22_proteinligandbenchmark
Science Score: 23.0%
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Repository
Dataset and evalutaion tools of the Shrec 2022 contest on protein-ligand binding site recognition
Basic Info
- Host: GitHub
- Owner: concept-lab
- Language: C
- Default Branch: master
- Size: 1.77 GB
Statistics
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
shrec22_proteinLigandBenchmark
Dataset and evalutaion tools of the Shrec 2022 contest on protein-ligand binding site recognition
Requirements
The script has been tested on Ubuntu 20.04.4 LTS and macOS Catalina 10.15.7.
Python3 must be installed
Python non-builtin modules
- numpy
If not installed: pip3 install numpy
C shared library installation
(recommended for OS)
Move in the installLIB folder and type ./install_script. This will compile the shared C library and move it in the main folder under the name: libCfunc.so
Usage
For evaluating putative pockets in PQR or as a boolean map for the vertices of the structure OFF format (TXT file):
If OFF format, in the working directory the "testData" folder must be present. This folder contains the structures in OFF format. It can be downloaded from https://github.com/concept-lab/shrec22_proteinLigandBenchmark.git
python3 evaluate.py <directoryName containing participant results>
Change in the script the fields pCoverageTH = 0.2 lCoverageTH = 0.5 to change the metric's threshold for the evaluation of a putative binding site(*).
Participant results are in the participantResults folder
Output of evaluation
rankStats.txt: file containing the ranking result (Top1, Top3, Top10 and metrics--LC and PC score as described in*)
failureList.txt: file containing the list of structure-ligands pairs not matched by any of the putative pockets.
Extra
The script filterLig.py, creates a folder containing all ligands (in xyz format) keeping only ligand atoms within 5A from any correspondent protein atom. These are actually the ligand coordinates used for evaluation (the same filtering process is performed within evaluate.py by providing the structures pqrs contained in the "allStructures" folder).
NOTE
A lighter version (without the full database and PQR structure files)of the contest's participants evaluation tool is provided in https://github.com/concept-lab/shrec22PLBindingevaluationTools.git
Full paper
https://arxiv.org/pdf/2206.06035.pdf
Cite
() L. Gagliardi et al, SHREC 2022: Protein-ligand binding site recognition, *Computers & Graphics https://doi.org/10.1016/j.cag.2022.07.005 (2022)
Owner
- Name: CONCEPT Lab @ IIT
- Login: concept-lab
- Kind: organization
- Location: Genova, Italy
- Website: https://concept.iit.it/
- Repositories: 5
- Profile: https://github.com/concept-lab