https://github.com/tsudalab/bpbi

Binding pose prediction by best arm identification
https://github.com/tsudalab/bpbi

Last synced: 3 months ago
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Binding pose prediction by best arm identification

• Host: GitHub
• URL: https://github.com/tsudalab/bpbi
• Owner: tsudalab
• Created: 2017-05-01T05:51:42.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-10-18T09:00:37.000Z (about 7 years ago)
• Last Synced: 2024-07-16T23:02:39.148Z (4 months ago)
• Language: Python
• Size: 12.2 MB
• Stars: 4
• Watchers: 7
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# bpbi

Binding Pose prediction as Best-arm Identification

# Required Packages 

python >= 2.7.x  

numpy >= 1.11.x  

pandas >= 1.11.x  

# Installation

Download or clone the github repository, e.g. git clone https://github.com/tsudalab/bpbi

# Usage 

Run test.py for searching the binding pose using best-arm identification algorithms.

# References

K. Terayama, H. Iwata, M. Araki, Y. Okuno, K. Tsuda, "Machine Learning Accelerates MD-based Binding-Pose Prediction between Ligands and Proteins", Bioinformatics, 2017. (https://doi.org/10.1093/bioinformatics/btx638)

Bubeck, S.; Munos, R.; Stoltz, G. "Pure exploration in multi-armed bandits problems." ALT, pp 23–37, 2009.  

Audibert, J.-Y.; Bubeck, S. "Best Arm Identification in Multi-Armed Bandits." COLT, 2010.  

Gabillon, V.; Ghavamzadeh, M.; Lazaric, A. "Best arm identification: A unified approach to fixed budget and fixed confidence." NIPS, pp.3212–3220, 2012.