Protein Visualization - Ribbon Diagram

This section provides a quick introduction of protein ribbon diagrams, which uses flat ribbon arrows for beta sheets, and twisted ribbon for alpha helices.

What Is Ribbon Diagram? - A ribbon diagram is a diagram to visualize a protein conformation using ribbons and wires to represent its secondary structures in 3-dimensions.

Here some common conventions used in protein ribbon diagram:

The picture below provides a good illustration of a protein ribbon diagram (source: uvm.edu). Note that two small molecules are included in the diagram showing how they are bonded (enclosed) in empty spaces inside the protein.

Visualization - Ribbon Diagram
Visualization - Ribbon Diagram

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

Protein and Amino Acid

 What Is Amino Acid

 The 20 Common Amino Acids

 Peptide, Peptide Bond, Amino Acid Residues

 What Is Protein

 Protein Structure Levels

 Alpha Helix and Beta Sheet

Protein Visualization - Ribbon Diagram

 Composed Proteins or Protein Complexes

 wwpdb.org - Worldwide PDB (Protein Data Bank)

 What Is FASTA

 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

 Full Version in PDF/EPUB