baba-hashimoto / gr-predictor

gr Predictor

"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.

Requirement

Python 3.6–, Anaconda, openbabel, dask, tesorflow

License

“gr Predictor” is available under the GNU General Public License.

Citing this work

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.

Contact

If you have any questions, please contact Takashi Yoshidome at [email protected].

Usage

• 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] )