py4chemoinformatics

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= Table of Contents :imagesdir: images

Update 03_2019: forked and tried to translate to english. Corrections are welcome.

Update 01_2020: updating the information to mimic original.

• https://asciidoctor.org/docs/asciidoc-syntax-quick-reference/#formatted-text[AsciiDoc Syntax Quick Reference]

== link:ch01_introduction.asciidoc[01 Introduction]

• What is RDKit?
• Target audience
• About the code in this book
• Acknowledgments
• bonus
• License

== link:ch02_installation.asciidoc[02 Create an environment for chemoinformatics]

• About Anaconda
• How to install Anaconda
• Build virtual environment and install packages
• Description of the installed package
• More about Conda

== link:ch03_python.asciidoc[03 Basics of Python programming]

• Python basics
• Use it conveniently with the Jupyter notebook
• Machine learning with Python

== link:ch04_database.asciidoc[04 Public database for chemoinformatics]

• ChEMBL
• PubChem
• Search for desired information with ChEMBL
• Other useful databases

== link:ch05_rdkit.asciidoc[05 Handling Structural Information with RDKit]

• What is SMILES?
• Let's draw the structure
• How to handle multiple compounds at once?
• Try hetero shuffling

== link:ch06_similarity.asciidoc[06 Evaluating the similarity of compounds]

• What does it mean that compounds are similar?
• Calculate similarity
• Virtual screening
• Clustering
• Structure Based Drug Design (SBDD)

== link:ch07_graph.asciidoc[07 Evaluation of similarity using graph structure]

• Classification by major skeleton (MCS)
• Matched Molecular Pair and Matched Molecular Series
• Visualize MMP networks using Cytoscape

== link:ch08_visualization.asciidoc[08 I want to have many compounds at once]

• Chemical Spaceとは
• Mapping using tSNE

== link:ch09_qsar.asciidoc[09 Basics of Quantitative Structure-Activity Relationship (QSAR)]

• Consider the cause of the effect (Classification problem)
• Predict the efficacy of drugs (regression problem)
• Model applicability (applicability domain)

== link:ch10_deeplearning.asciidoc[10 Introduction to Deep-Learning]

• About TensorFlow and Keras
• Google colab
• Let's install

== link:ch11_dlqsar.asciidoc[11 Structure-activity relationship using deep-learning]

• Predictive model construction using DNN
• Devising a descriptor (neural fingerprint)

== link:ch12_generativemodels.asciidoc[12 Let the computer think about chemical structure]

• Preparation
• Illustration

== link:ch13_beyond.asciidoc[13 Conclusion]

• Final remarks and further reading

== License

This document is copyright (C) 2019 by @fmkz___ and @iwatobipen

This document is link:https://github.com/Mishima-syk/py4chemoinformatics/blob/master/LICENSE[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License].

image::by-nc-sa.png[CC-BY-NC-SA, width=100]