Molecule Tutorials - Herong's Tutorial Examples
∟References
List of reference materials used in this book.
- 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
- On Exploring Structure Activity Relationships, Rajarshi Guha,
ncbi.nlm.nih.gov/pmc/articles/PMC4852705
- 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
- Open Babel: The Open Source Chemistry Toolbox,
sourceforge.net/projects/openbabel
- 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
Table of Contents
About This Book
Introduction of Molecules
Molecule Names and Identifications
Molecule Mass and Weight
Protein and Amino Acid
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
Gene and Chromosome
Protein Kinase (PK)
DNA Sequencing
Gene Mutation
SDF (Structure Data File)
PyMol Installation
PyMol GUI and CLI
PyMol Selections
PyMol Editing Functions
PyMol Measurement Functions
PyMol Movie Functions
PyMol Python Integration
PyMol Object Functions
ChEMBL Database - European Molecular Biology Laboratory
PubChem Database - National Library of Medicine
PDB (Protein Data Bank)
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)
Relocated Tutorials
Resources and Tools
Molecule Related Terminologies
►References
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