Table of Contents
Update 03_2019: forked and tried to translate to english. Corrections are welcome.
Update 01_2020: updating the information to mimic original.
01 Introduction
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What is RDKit?
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Target audience
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About the code in this book
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Acknowledgments
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bonus
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License
02 Create an environment for chemoinformatics
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About Anaconda
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How to install Anaconda
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Build virtual environment and install packages
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Description of the installed package
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More about Conda
03 Basics of Python programming
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Python basics
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Use it conveniently with the Jupyter notebook
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Machine learning with Python
04 Public database for chemoinformatics
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ChEMBL
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PubChem
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Search for desired information with ChEMBL
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Other useful databases
05 Handling Structural Information with RDKit
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What is SMILES?
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Let’s draw the structure
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How to handle multiple compounds at once?
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Try hetero shuffling
06 Evaluating the similarity of compounds
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What does it mean that compounds are similar?
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Calculate similarity
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Virtual screening
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Clustering
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Structure Based Drug Design (SBDD)
07 Evaluation of similarity using graph structure
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Classification by major skeleton (MCS)
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Matched Molecular Pair and Matched Molecular Series
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Visualize MMP networks using Cytoscape
08 I want to have many compounds at once
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Chemical Spaceとは
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Mapping using tSNE
09 Basics of Quantitative Structure-Activity Relationship (QSAR)
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Consider the cause of the effect (Classification problem)
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Predict the efficacy of drugs (regression problem)
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Model applicability (applicability domain)
10 Introduction to Deep-Learning
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About TensorFlow and Keras
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Google colab
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Let’s install
11 Structure-activity relationship using deep-learning
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Predictive model construction using DNN
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Devising a descriptor (neural fingerprint)
12 Let the computer think about chemical structure
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Preparation
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Illustration
13 Conclusion
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Final remarks and further reading
License
This document is copyright © 2019 by @fmkz___ and @iwatobipen