"gr Predictor" is a deep-learning model rapidly estimating the water-oxygen distribution function around protein obtained by the 3D-RISM theory from the protein 3D structure. The computation is completed within a few minutes when using a single CPU and approximately one minute when using a single GPU.
Python 3.6–, Anaconda, openbabel, dask, tesorflow
“gr Predictor” is available under the GNU General Public License.
If you use “gr Predictor”, please cite:
gr Predictor: a Deep-Learning Model for Predicting the Hydration Structures around Proteins
Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi, Masateru Ohta, and Takashi Yoshidome
bioRxiv 2022.04.18.488616; doi: https://www.biorxiv.org/content/10.1101/2022.04.18.488616v1.
If you have any questions, please contact Takashi Yoshidome at [email protected].
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Import modules
import guv_prediction as gpred -
Prediction of g(r)
spliter = gpred.Prediction( pdb_dir, dx_dir, pred_area_center = np.array([x, y, z]), pred_area_range = w )-
pdb_dir: Path to the PDB file -
dx_dir: Path to the output file (dx format) -
pred_area_center: Central coordinate of the prediction region in the protein ( x, y, and z [angstrom] ) -
pred_area_range: Width of the prediction region ( w [angstrom] )
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