Biological Macromolecules

Molecular Case Studies

• Biomolecular Building Blocks: Atoms, Bonds, and Conformations
• Amino Acids: Types and Properties
• Types of Chemical Interactions in Biology
  • Noncovalent Interactions: Overviews
    • Electrostatic force (Part 1) (v) and
    • Partial charges and inter-molecular forces comparisons (Part 2) (v)
  • What are ...
    • Disulfide bonds (v)
    • Hydrogen bonds (v)
    • Ionic bonds/Salt Bridges
    • Pi interactions
    • Halogen bonds (v)
    • Hydrophobic interactions
  • Chemical Bonds in a Macromolecular Structure (example gamma Chymotrypsin) (v)
• What is a Protein? (w+v)

  The Molecular Case Study Cycle (2020)

Exploring Protein Data Bank

Molecular Visualization Tools

Bioinformatics: Data, Tools, and Resources

• Methods for Determining Atomic Structures (w)
• Understanding PDB data (w)
• Entry, Entity, Assembly, and Instance (v)
• What is in the PDB File? (v)
• Exploring a PDB entry (w, see related pages)
• Navigating the Structure Summary Page (v)
• Coordinate files in PDB and PDBx/mmCIF Format (w)
• Missing coordinates (w)
• Biological assemblies (w)
• Molecular Visualization Conventions: Representations of Atoms, Bonds, and Molecules (v)
• Ligands in the PDB (w)

• Mol*
  • Intro Guide (v); Exploring Overall Shape and Local Environments (v);  Documentation (w); Cheat Sheet (d)
• Chimera
  • Basics (v); Menus (v); Selecting atoms, residues and chains (v); Structure analysis (v); Structure Comparisons (v); Cheat Sheet (d) 
• iCn3D
  • Tutorials - Part 1 (windows, menus, representations) (v) and Part 2 (interactions, alignment, embedding) (v)
• Jmol
  • Intro to Jmol scripting (w); Jmol/JSmol documentation (w) ; Jmol Mouse Commands (w); Cheat Sheet (d)
• Pymol
  • Intro to Pymol via Webinar (v); Practical Pymol for beginners (w)

• Sequence, Structure, and Function
• Resources and Tools of Interest
  • Resources/Tools commonly used in molecular case studies
  • Detailed lists (w)
  • Protein Sequences: UniProt (r)
    • How to use UNP (v playlist); The PDB-UniProt Connection (v)
  • Nucleotide BLAST - find gene + search similar
    • At NCBI (v)
  • Protein BLAST - sequence based searches
    • At NCBI (v); At UniProt (v)
  • Scientific Literature:
    • PubMed (An older video) (v); The PDB-PubMed Connection.
    • NCBI BookShelf (v playlist)
  • Drug information: DrugBank
    • An older video about DrugBank (v)
  • KEGG
    • KEGG Pathways Database (v)

Case Studies

• Why use Case Studies?
  • For Students
  • For Teachers
• Are you new to Case Studies?
  • Learn about Case Types & Methods
• Do you wish to learn more about Case Studies?
  • Check out related Publications

Authoring Molecular Case Studies

• Molecular Case Studies - Idea Bank (created 2022)
• Students authoring Molecular Case Studies - Guidelines; Pilot Implementations (2021)
• Educators authoring Molecular Case Studies - Guidelines (2021)
• Rubrics for reviewing and publishing Molecular Case Studies at Molecular CaseNet (2021)
• General guidelines (2019)