py4chemoinformatics

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= Table of Contents :imagesdir: images

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

I added a little (2018.12.12). Since the web interface is likely to be beyond the scope of introductory, I will consider how to do it.

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

image::python_for_ci.png[py4chemoinformatics, width=250]

== link:ch01_introduction.asciidoc[01 Introduction]

• What is chemoinformatics?
• What is RDKit?
• Target audience
• Acknowledgment
• License

== link:ch02_installation.asciidoc[02 Let's prepare the environment for chemoinformatics]

• Anaconda(Python, Jupyter, scikit-learn)
• RDKit

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

• Python basics
• Let's use it conveniently with Jupyter notebook
• To do machine learning with Python

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

• ChEMBL
• PubChem
• Search for the information you want on ChEMBL

== 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?

== link:ch06_similarity.asciidoc[06 Try to evaluate the similarity of compounds]

• Descriptor, fingerprint
• Calculate similarity
• Virtual screening

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

• Classification by major skeleton (MCS)
• Compound Network by Matched Molecular Pair
• 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
• I will devise a descriptor (neural fingerprint)

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

• Structure generation using Recurrent Neural Network

== link:ch13_beyond.asciidoc[13 Conclusion]

• Final remarks and further reading