Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy
| Dataset/Database | Type | Composition | url | Time |
|---|---|---|---|---|
| DeepSequence dataset | Fitness | 34 single-point mutation DMS studies | 2018-09 | |
| MaveDB | Fitness | The database contains fitness data of different mutations | https://www.mavedb.org/ | 2022-09 |
| GeoFitness dataset | Fitness | 74 DMS datasets | dms.csv | 2023-05 |
| ProThermDB | ΔΔG and ΔTm | The database contains ΔΔG and ΔTm data of different mutations | https://web.iitm.ac.in/bioinfo2/prothermdb/index.html | 2021-07 |
| ThermoMutDB | ΔΔG and ΔTm | The database contains ΔΔG and ΔTm data of different mutations | https://biosig.lab.uq.edu.au/thermomutdb/ | 2021-07 |
| S2648 | ΔΔG | 2648 single-point mutation from 131 proteins | This file is included in S8754.csv | 2009-08 |
| S8754 | ΔΔG | 8754 single-point mutation from 301 proteins | S8754.csv | 2023-05 |
| S783 | ΔΔG | 783 single-point mutation from 55 proteins | S783.csv | 2023-05 |
| S669 | ΔΔG | 669 single-point mutation from 94 proteins | S669.csv | 2022-01 |
| S461 | ΔΔG | 461 single-point mutation from 48 proteins | S461.csv | 2023-01 |
| S1626 | ΔTm | 1626 single-point mutation from 95 proteins | This file is included in S4346.csv | 2016-06 |
| S4346 | ΔTm | 4346 single-point mutation from 349 proteins | S4346.csv | 2023-05 |
| S571 | ΔTm | 571 single-point mutation from 37 proteins | S571.csv | 2023-05 |
Other data files in the data folder
- download
GeoStab
git clone https://github.com/Gonglab-THU/GeoStab.git
cd GeoStab-
install
FoldXsoftware -
install
Anacondasoftware -
install Python packages from
Anaconda
conda create -n geostab python=3.10
conda activate geostab
conda install pytorch cpuonly -c pytorch
pip install biopandas
pip install biopython
pip install click
pip install pdb-tools- You should modify the mutant information in
generate_example_mut_info_csv.py(0 <= pH <= 11 and 0 <= temperature <= 120) - You should modify the
software_foldxinrun.sh - You should install
AlphaFold2and modify script inrun.shto generateSeqversion structure
# fitness Seq prediction
python generate_example_mut_info_csv.py
bash run.sh -m fitness -v Seq -o ./example_Seq
# fitness 3D prediction
python generate_example_mut_info_csv.py
bash run.sh -m fitness -v threeD -o ./example_3D
# ΔΔG/ΔTm Seq prediction
python generate_example_mut_info_csv.py
bash run.sh -m ddGdTm -v Seq -o ./example_Seq
# ΔΔG/ΔTm 3D prediction
python generate_example_mut_info_csv.py
bash run.sh -m ddGdTm -v threeD -o ./example_3D