Protein 3D Structure Visualization & Structural Bioinformatics
Graduate School of Frontier Biosciences, Osaka University (Japan), June 26-30, 2006

  Seminar Room 3F, Nanobiology Building Computer Lab, Engineering School
AM - Morning
PM - Afternoon
Monday June 26 10:40-12:10   14:40-17:50
Tuesday June 27     13:00-17:50
Wednesday June 28     13:00-17:50
Thursday June 29 9:00-12:10   Librarian 14:40-17:50
Friday June 30   13:00-17:50  
Organizer: Professor Keiichi Namba.
Lead Instructor: Eric Martz
(Main author of FirstGlance in Jmol and Protein Explorer - Prof. Emeritus, Univ. Mass. Amherst;
with co-instructors Yukihiro Miyanaga, Yoshihiko Fujimura, Nao Moriya.
Thanks to Kana Moriya for arrangements.
This document is on-line: At click on Workshops, or

Rationale & Goals: In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. This workshop will enable participants to find published macromolecular structure data, and visualize and interpret 3D macromolecular structure. Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their teaching and research. Those who wish can prepare interactive macromolecular structure presentations, such as those at MolSlides.Org.

Software: The central tools for this workshop (all free) are:
FirstGlance in Jmol (
and Jmol java applet
  • Operates in all popular browsers and platforms, including Windows, OSX, and linux.
  • Operates on-line only.
  • Open source.
  • Assumes that you are already familiar with principles of protein structure.

    Adopted by Nature Structural and Molecular Biology and other bioinformatics resources.
    Built with the free, open source Jmol java applet.
    Protein Explorer in Chime (
    and Chime plugin
  • Operation limited to Windows or Mac Classic.
  • Operates on-line or off-line (downloaded).
  • Open source.
  • Much more powerful than FirstGlance. Extensive help and reference materials useful to both students and researchers. Much easier to use, yet much more powerful than RasMol. Won the 2003 MERLOT Classic Award in Biology for exemplary online learning resources: "The Protein Explorer has revolutionized the teaching of biology at a molecular level". Able to build MolSlides. Adopted by numerous bioinformatics resources. Built with the free MDL Chime plugin (source code not open).

    Level & Pace: This workshop is designed for graduate students and researchers familiar with basic biochemistry, but with no previous molecular visualization software experience. It progresses rapidly to powerful tools that will be of interest to specialists in protein structure and bioinformatics. Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power to discover within Protein Explorer and its connections to complementary structural bioinformatics resources!

    Day 1 Morning 10:40-12:10, Monday June 26. Seminar Room.
        Review of Protein Chemistry and Structure.
        Introduction to Structural Bioinformatics.

      Review of Protein Chemistry and Structure.
    1. Central Dogma: DNA mRNA Protein.
    2. 20 Amino acids
    3. Polypeptide chain geometry and steric restrictions
    4. Covalent and non-covalent chemical bonds
    5. Secondary Structure
    6. Folding: hydrophobic collapse
    7. Protein folds cannot be reliably predicted from theory

    8. Introduction to Structural Bioinformatics

    Day 1 Afternoon 14:40-17:50, Monday June 26. Computer Lab.
        FirstGlance in Jmol for basic macromolecular visualization.
        Finding published molecules of interest.

      This afternoon, work in linux, in Mozilla or Firefox.

    1. At, enter 1PGB (a Protein Data Bank identification code). Try these controls:
      1. Introduction
      2. and
      3. Top 2 rows of views
      4. Vines
      5. Buttons
      6. Center Atom
      7. Reset
      8. More Views
        • Cation-pi interactions and salt bridges (1AXI, 1M4U PQS for inter-chain)
        • Distances
        • Color by uncertainty
    2. Explore 1HHO in, especially:
      1. Ligands button
      2. for full names of ligands
      3. Hide
      4. Find (explain the distributions of gly, pro, ala, glu, phe, viewed one at a time)
      5. Contacts to HEM
    3. 1BKX: More Views, Non-standard amino acids
    4. 2ACE:

    5. Finding published molecules of interest:
      1. Atlas of MacroMolecules:
      2. PDB at a Glance:

      3. PDB Lite:
      4. Advanced search engines at the World Wide Protein Data Bank (
      5. OCA (Israel)

    Day 2, 13:00-17:50 Tuesday June 27. Computer Lab.
        Protein Explorer.
        Saving MolSlides.
        Exploring Your Molecule.


      This afternoon, work in Windows ME (virtual machine under linux) for compatibility with Chime and Protein Explorer.
      Use Firefox (or Netscape 7.2 or Mozilla). Go to to use the latest version, PE 2.78 Alpha (June, 2006).
      Skip the PE Demo Movies -- use them for review (if you haven't used PE for a few months) or to start friends who didn't attend this course.

      PE: FirstView

    1. Click Quick-Start ... to display Gal4:DNA.
    2. Organization of PE into 3 frames: control panel, molecular image, and messages.
    3. Use the mouse to rotate the molecule; click to identify atoms.

      PE: Features of the Molecule

    4. Understanding and using information provided in the PDB file header by the authors of the structure.
    5. Enter 1E3Q in slot at FrontDoor (it has all Features).
    6. The Help/Index/Glossary (green for "go"), a major component of PE's knowledge base.

    7. Undo, History

      Saving MolSlides

    8. Detailed Procedure for Saving MolSlides
    9. Save This View, Add a MolSlide
    10. MolSlide Manager, taking notes in MolSlides
    11. Exporting & Saving MolSlides to your disk
    12. Viewing MolSlides

      PE: QuickViews

    13. Selecting, emphasizing, and hiding portions of the molecule.
    14. Selecting arbitrary atoms/chains/residues by clicking on them.
    15. Saving/recalling selected sets.
    16. Zooming, centering.
    17. Backbone, trace, cartoon, stick, ball and stick, spacefill to van der Waals radii.
    18. Coloring by element (Corey, Pauling, Koltun color scheme).
    19. Coloring cartoons by secondary structure.
    20. Identifying the amino and carboxy termini (5', 3' ends): N->C Rainbow (Group) color scheme.
    21. Interpreting the distribution of hydrophobic, polar, and charged residues (Polarity color schemes).
      1. Potassium channel: 1bl8. Trp prefers lipid-water interface.
      2. Gramicidin in a lipid bilayer: bilagram.pdb
    22. Coloring to distinguish A, T, G, C, U. How to distinguish DNA from RNA. (Cf. 104d)
    23. Coloring by disorder: temperature factor coloring.   Thermal vs. static disorder.

    24. PE Site Map

    25. Explore Your Molecule
    Day 3, 13:00-17:50 Wednesday June 28. Computer Lab.
        Sequence to 3D Mapping.
        Evolutionary Conservation: ConSurf Server.
        All-Atom Contact Analysis: MolProbity Server.
        Saving/Restoring a PE Session.
        Advanced PE Features.


    This afternoon, continue in Windows ME (virtual machine under linux) for compatibility with Chime and Protein Explorer.
    Items in gray were not done.
      Residue sequence ranges for the CDR's in the Fab of 1FDL are:
        Heavy chain (H)
      • CDR1: 31-35
      • CDR2: 50-66
      • CDR3: 98-105

        Light chain (L)

      • CDR1: 24-34
      • CDR2: 50-56
      • CDR3: 90-97
      For shortcuts and tricks in using PE to visualize epitope-paratope contacts, see step #35 in this Antibody Structure Tutorial.


    1. Protein Explorer's clickable Seq3D
      1. Sequence to 3D structure mapping.
      2. Finding all instances of one amino acid (e.g. cysteine).
      3. Selecting and coloring an arbitrary range of residues (see example in box at right).

    2. PE's MSA3D (via PE Site Map, Advanced Explorer): Introduction to multiple sequence alignments (for ConSurf).

    3. External Resources (via PE Site Map): Structural Bioinformatics Servers that complement PE.
      1. ConSurf: regions conserved or hypermutable in evolution
      2. MolProbity: all-atom contact analysis -- add hydrogens, then
        • See and correct Asn, Gln, His side-chain flips
        • See atomic clashes and evaluate overall clash score (1cbx)

    4. Importing and Applying MolSlides: Saving a PE Session.

    5. Multiple-Model NMR Results (1JSA, 1CFC)
      1. Most representative model (via PE Site Map -> External Resources).
      2. NMR Control Panel.
      3. Animation simulates thermal motion (Click "Animations" at the FrontDoor).

    6. Noncovalent Bonds: Contact-Decorated Surfaces. Example: Gal4 contacting DNA (1d66), showing:
      1. Sequence specific recognition DNA bases by zinc finger domain of protein
      2. Hydrophobic protein-protein interaction
      3. Nonspecific charge interactions at DNA backbone phosphates

    7. Preferences in Protein Explorer (beneath the message box).
    8. Aliases for RasMol/Chime commands (beneath the message box).

    9. QuickViews Boolean (scroll down in the QuickViews control panel).
      1. Example: In 1FDL, display Fab atoms contacting lysozyme, then overlay (DISPLAY) a cartoon display of all protein. Color the cartoon by Chain, then by N->C Rainbow, then by Structure.
    Day 4, Morning 9:00-12:10, Thursday June 29. Seminar Room.
        Challenge Questions
        Structural Genomics.
        Structure Conservation.
        Specific Oligomers vs. Crystal Contacts
        Animations and Morphing
    Today we will spend a large amount of time answering questions ("challenges") about structures. Use either FirstGlance in Jmol or Protein Explorer, whichever gives the answer more easily.
    1. Challenges. (The challenge questions will be given during class. They are not on-line.)

    2. Structural Genomics: Worldwide Protein 3D Structure Knowledge
      1. How are 3D macromolecular structures obtained? Crystallography, NMR, and homology modeling.
      2. What fraction of the human proteome has known structure? A few percent.
      3. Is Structural Genomics the answer? Not in the next few years.
      4. Intrinsicially unstructured proteins:
          About 10% of proteins are thought to be fully disordered to support their functions, and 40% of eukaryotic proteins have at least one long disordered region. Examples.

    3. Searching by structure without reference to sequence: (Try the bacterial cell division protein 1FSZ§.)
      Structure is more conserved than sequence! (Chothia et al., 2003; Precis)
      1. Shindyalov & Bourne's Combinatorial Extension
      2. NCBI's Vector Alignment Search Tool (VAST)
      Model of SV40


    4. Specific Oligomers vs. Crystal Contacts

    5. Animations & Morphing (Click "Animations" at PE's FrontDoor).
      1. Animation of NMR ensembles of models to simulate thermal motion
      2. Animation of ligand binding (HIV protease inhibitor; protein bending DNA)
      3. Morphing conformational changes
    Day 4, Afternoon 14:40-17:50, Thursday June 29. Computer Lab.

    [Librarian's class. Not part of protein structure class.]

    Day 5, 13:00-17:50 Friday June 30 - Seminar Room.:
        Educators' Resources.
        Molecular Modeling.
    Again, today we will spend a large amount of time answering questions ("challenges") about structures. Use either FirstGlance in Jmol or Protein Explorer, whichever gives the answer more easily.

    1. Challenges.

      For Educators

    2. Lesson Plans (at PE's FrontDoor)

    3. About Protein Structure (at PE's FrontDoor)

    4. World Index of Molecular Visualization Resources
      1. Hundreds of Chime-based tutorials indexed by macromolecule
      2. Chime-based resources en Español
      3. Sources of atomic coordinate (PDB) files (metabolites, inorganic crystals, lipid micelles, etc.)
      4. Galleries, Molecular Sculpture and Physical Models, Software

    5. MolViz.Org
      1. BioMolecular Explorer 3D (for students ages 15-19). Soon to be available on CD with Chime and Netscape 4.8 installers.
      2. Amino Acid Quizzer
      3. DNA, Hemoglobin, Antibody, MHC
      4. Lipid Bilayers and Gramicidin Channel
      5. IR Spectra with animated vibrations
      6. Toobers in Science Education
      7. History of Visualization of Biological Macromolecules
          Where did Chime come from? What about Fred's Folly and Byron's Bender? See early computer images, physical models including the latest by computer-driven laser-powered rapid-prototype engineering, and the latest molecular sculpture.
      8. Knots in Proteins

    6. Building a web page with hyperlinks to Protein Explorer that prespecify molecules for your teaching or research. Examples.   Methods.   Detailed methods.

    7. Modeling vs. Visualization

      Optional Topics by Participants' Request -- Time Permitting (or Later Private Sessions):

    8. Homology (comparative) modeling: Introduction.

    9. Aligning two or more chains or molecules, and how to view the alignment.
      1. The CE site will align any two protein chains quickly and easily (but hetero atoms are discarded).
      2. DeepView can align anything (one or more than one chains), selecting any subset of atoms for the alignment (other atoms following), and retaining hetero atoms. The results can be saved as a PDB file, but will need manual editing to separate models with MODEL [N] and ENDMDL records so that Protein Explorer can distinguish the models. Gale Rhodes provides a DeepView tutorial: click on the section Comparing Proteins.

    10. Mutating your model:
      1. Changing residue sidechains and rotamer minimization with DeepView
      2. DeepView beginners should start with the superb Molecular Modeling for Beginners by Gale Rhodes, Univ. Southern Maine.
      3. DeepView resources are indexed at

    Keep in touch!

    § Example 1FSZ thanks to Gabe McCool. See also his presentation on 1FSZ in PE.