Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
Molecule Tutorials - Herong's Tutorial Examples
https://www.herongyang.com/Molecule
Copyright © 2019-2023 Herong Yang. All rights reserved.
This book is a collection of notes and tutorial examples written by the author while he was learning molecules and related tools. Topics include understanding atoms, bonds and molecules; introduction of atomic isotopes and elements; introduction of proteins and amino acids; introduction of protein kinases; molecule SDF (Structure Data File) format; generating PNG pictures from molecule SDF files; installing RDkit as molecule tool; visualizing molecule structure in 3-D with PyMol; generating molecule movie with PyMol. Updated in 2023 (Version v1.26) with minor updates.
Table of Contents
Molecule Names and Identifications
InChI (International Chemical Identifier)
Peptide, Peptide Bond, Amino Acid Residues
Protein Visualization - Ribbon Diagram
Composed Proteins or Protein Complexes
wwpdb.org - Worldwide PDB (Protein Data Bank)
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
What Is RNA (Ribonucleic Acid)
What Is DNA (Deoxyribonucleic Acid)
DNA Primary Structure - Double Helix
What Is DNA/RNA Base and Sequence Pair
Gene Expression - Building Proteins
Genetic Transcription - Creating mRNA
Genetic Translation - Creating Protein
DNA Gene Sequence - Exons and Introns
Chromosome Replication (or DNA Replication)
What Is PCR (Polymerase Chain Reaction)
What Is Sanger Sequencing Method
What Is NGS (Next-Generation Sequencing)
Base-Pair Insertion and Deletion
Gene Mutation Inheritance Likelihood
What Is VCF (Variant Calling Format)
"vcftools" - VCF Utility Command
What Is VAF (Variant Allele Frequency)
Gene Mutation Naming Convention
What Is SDF (Structure Data File)
Convert SDF to SVG using Open Babel
"sdf2svg" - PHP Script to Convert SDF to SVG
Install PyMol Incentive Edition on macOS
Install PyMol Open Source Edition
Install Open Source PyMol with Homedrew
Install Open Source PyMol with Fink
Load Molecule from File into PyMol
Virtual Trackball Rotation on PyMol
"load" and "delete" Commands on PyMol
"log_open" and "log_close" Commands on PyMol
Model Space and Camera Space on PyMol
"get_view" and "set_view" on PyMol
View Parameters Auto Adjusted on PyMol
Rotation with Transformation Matrix
Difference of "turn" and "rotate" Commands
Difference of "move" and "translate" Commands
"center", "zoom" and "reset" Commands
Model-to-Camera Space Coordinates Mapping
Camera-to-Model Space Coordinates Mapping
"show lines" Presentation Command
"show sticks" Presentation Command
"show spheres" Presentation Command
"show surface" Presentation Command
"show mesh" Presentation Command
Create Selection with Mouse in PyMol
Substructure Selection Visualization in PyMol
Modify Molecule Structure in PyMol
Export Molecule Substructure in PyMol
Create Methane Molecule in PyMol
"pk1", "pk2", "pk3" and "pk4" Selections
"edit id n1, id n2, id n3, id n4" Commands
"remove pk*" and "remove_picked" Commands
"unbond pk1, pk2" and "bond pk1, pk2" Commands
"replace new_atom, ..." Replace pk1 with New Atom
"attach new_atom, ..." Attach to pk1 with New Atom
Build Alcohol Molecule with PyMol
"get_extent" - Picked Atom Location
"label" - Generate Labels on Atoms
Distance between Atoms in PyMol
Angle Formed by 3 Atoms in PyMol
Dihedral Angle Formed by 3 Atoms in PyMol
Use Selection Expressions in PyMol
"get_area" - Surface Areas of Atoms
Surface Area of Entire Molecule
"get_position" - Viewing Center
Run Python Statements from PyMol
Launch PyMol from Python Interpreter
PyMol Python API Only Functions
Visualize Objects Independently
ChEMBL Database - European Molecular Biology Laboratory
Call ChEMBL Data Web Service Directly
ChEMBL Data Resource - molecule
ChEMBL Data Resource - activity
ChEMBL Data Resource - document
ChEMBL Data Resource - chembl_id_lookup
chembl_webresource_client - Python Client
chembl_webresource_client - Usage Examples
chembl_webresource_client - RetryError Exception
PubChem Database - National Library of Medicine
What Is PDB (Protein Data Bank)
What Is CRSB (Research Collaboratory for Structural Bioinformatics)
What Is PDBe (Protein Data Bank in Europe)
What Is PDBj (Protein Data Bank Japan)
INSDC (International Nucleotide Sequence Database Collaboration)
Reference Genome Sequence Data File
RefSeq Proteins of Human Genome
HGNC (HUGO Gene Nomenclature Committee)
Human Gene Symbol Report by HGNC
Synchronization with HGNC Database
Keywords: Molecule, DNA, Gene, Protein, BioTech