Cheminformatics Tutorials - Herong's Tutorial Examples
∟References
This section provides a list of reference materials used in this book.
- SMILES - A Simplified Chemical Language,
daylight.com/dayhtml/doc/theory/theory.smiles.html
- RDKit: Open-Source Cheminformatics Software,
rdkit.org
- RDKit GitHub Site - Source Code and Tutorials,
github.com/rdkit
- Open Babel: The Open Source Chemistry Toolbox,
openbabel.org
- Open Babel Command Manuals and Tutorials,
openbabel.org/wiki/Category:Guides
- THE IUPAC INTERNATIONAL CHEMICAL IDENTIFIER (INCHI), IUPAC,
iupac.org/who-we-are/divisions/division-details/inchi/
- PubChem, National Library of Medicine,
pubchem.ncbi.nlm.nih.gov
- ChEMBL, European Molecular Biology Laboratory,
ebi.ac.uk/chembl/
- PubChem structure-activity relationship (SAR) clusters, Sunghwan Kim, et al.,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492103/
- PubChem structure-activity relationship (SAR) clusters, Sunghwan Kim, et al.,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492103/
- Worldwide PDB (Protein Data Bank),
https://www.wwpdb.org
- Human Proteome Map (HPM) Portal,
http://humanproteomemap.org
- Universal Protein Resource (UniProt),
https://www.uniprot.org
- CTfile Formats, Accelrys Software,
download.accelrys.com/freeware/ctfile-formats/
- What is the correct format for compounds in SDF or MOL files?, Nonlinear Dynamics,
nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx
- PyMOLWiki,
pymolwiki.org/
- PyMol, Schrodinger,
pymol.org
- Introduction to PyMOL,
pitt.edu/~epolinko/IntroPyMOL.pdf
- A Beginner’s Guide to Molecular Visualization Using PyMOL, Nicholas Fitzkee,
folding.chemistry.msstate.edu/files/bootcamp/2019/session-08_pymol-tutorial.pdf
- Jmol: an open-source Java viewer for chemical structures in 3D,
jmol.sourceforge.net
- Getting Started with Jmol,
cbm.msoe.edu/includes/modules/jmolTutorial/jmolGettingStarted.html
- Pharmacodynamics, Alex Yartsev,
derangedphysiology.com/main/cicm-primary-exam/required-reading/pharmacodynamics
- Fingerprints - Screening and Similarity, Chemaxon,
daylight.com/dayhtml/doc/theory/theory.finger.html
- Chemical Fingerprints,
B Zagidullin, et al.,
docs.chemaxon.com/display/docs/chemical-fingerprints.md
- Comparative analysis of molecular fingerprints in prediction of drug combination effects,
B Zagidullin, et al.,
academic.oup.com/bib/article/22/6/bbab291/6353238
Table of Contents
About This Book
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
Using Open Babel Command: "obabel"
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction
Resources and Tools
Cheminformatics Related Terminologies
►References
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