Published December 11, 2020 | Version v1.0.1-0
Software Open

DEFMap: Dynamics Extraction From cryo-em Map

Creators

  • 1. Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub
  • 2. Graduate School of Pharmaceutical Science, Kyoto University
  • 3. Graduate School of Medicine, Kyoto University
  • 4. Institute for Protein Research, Osaka University
  • 5. Graduate School of Medical Life Science, Yokohama City University

Description

This version contains clinfo/DEFMap (version: v1.0.1) and leave-one-out cross-validation (LOOCV) dataset (corresponding input test data and trained models) used in this paper. If you want to use the LOOCV models, refer to the inference command in README and replace the input and model with those in the LOOCV dataset.  

e.g.

python 3dcnn_main.py infer --test_dataset loocv_data/test_input_data/test_fold_1.jbl -o loocv_data/trained_model/model_kf1.h5 --prediction_output result/prediction_kf1.jbl

The joblib output file contains a python dictionary object (key: voxel coordinate, value: logarithm of RMSF), and a voxel-level correlation coefficient is calculated and displayed.
 

Files

clinfo/DEFMap-v1.0.1.zip

Files (2.2 GB)

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Additional details

Related works

Is supplement to
https://github.com/clinfo/DEFMap/tree/v1.0.1 (URL)