Protein 3D Structure Visualization & Structural Bioinformatics
Graduate School of Frontier Biosciences, Osaka University (Japan), May 28-June 4, 2007

Schedule of Times and Rooms

Lead Instructor: Eric Martz
(Author of FirstGlance in Jmol and Protein Explorer - Prof. Emeritus, Univ. Mass. Amherst;
Organizer and Co-Instructor: Professor Keiichi Namba.
with teaching assistants Nao Moriya, Takashi Fujii, Masafumi Shimada.
Thanks to Kana Moriya for arrangements.
This document is on-line at

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.

    Exceptional ease of use. Limited set of "canned" views.

    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 (including on Intel Mac OS X).
  • Operates on-line or off-line (downloaded).
  • Open source.
  • Much more powerful than FirstGlance: fully customizable images with surfaces. Extensive help and reference materials useful to both students and researchers. Helps you understand and interpret. 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).

    Day 1, Morning 10:30-12:00, Monday May 28. Nanobiology Seminar Room 3F.
        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 May 28. Computer Lab, GSE Common 2F.
        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:   Thermal vs. static disorder ("temperature").
    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
      6. Probable Quaternary Structure Server: Specific Oligomers.
    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 Morning 10:30-12:00, Tuesday May 29. Nanobiology Seminar Room 3F.
        Structural Bioinformatics and Genomics.
        Homology (Comparative) Modeling
    1. Jmol in Scientific Journals
      1. FirstGlance in Jmol: Nature Structural and Molecular Biology
      2. "Jmolized" Journal Figures: ACS Chemical Biology
      3. Jmolize your own figures: Frieda Reichsman -- MoleculesInMotion.Com

    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. Modeling vs. Visualization

    4. Homology (comparative) modeling: Introduction.
      1. Automated homology modeling: submit sequences to Swiss-Model (click on First Approach Mode).
    Day 2, Afternoon, 13:00-17:50 Tuesday May 29. Computer Lab, GSE Common 2F.
        Protein Explorer: Customized Molecular Views.
        Creating MolSlides.

      This afternoon, work in Windows ME (virtual machine under linux) for compatibility with Chime and Protein Explorer.
      Use Mozilla Firefox. Go to to use the latest version, PE 2.80 (May, 2007).
      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

    8. Save any molecule you see! (as a PDB file)
    9. Saving MolSlides
      1. Detailed Procedure for Saving MolSlides
      2. Save This View, Add a MolSlide
      3. MolSlide Manager, taking notes in MolSlides
      4. Exporting & Saving MolSlides to your disk
      5. Viewing MolSlides
      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.

    10. PE: QuickViews
        Basics (can do in FirstGlance in Jmol)
      1. Selecting, emphasizing, and hiding portions of the molecule.
      2. Selecting arbitrary atoms/chains/residues by clicking on them.
      3. Saving/recalling selected sets.
      4. Zooming, centering.
      5. Backbone, trace, cartoon, stick, ball and stick, spacefill to van der Waals radii.
      6. Coloring by element (Corey, Pauling, Koltun color scheme).
      7. Coloring cartoons by secondary structure.
      8. Identifying the amino and carboxy termini (5', 3' ends): N->C Rainbow (Group) color scheme.

        Cannot do in FirstGlance in Jmol (yet)
      9. DISPLAY, Surface.
      10. Two or more surfaces? PE Site Map, Advanced Explorer, Surfaces.
      11. (More things you cannot yet do in FirstGlance are below.)

      12. Example: Gramicidin in a lipid bilayer: bilagram.pdb
        • Toggle water, ligands. (These views can be done in FirstGlance in Jmol.)
        • Display protein as ball and stick, color by Polarity 2 and 3.

    11. PE Site Map

    12. Sequences: Protein Explorer's clickable Seq3D
      1. Sequence to 3D structure mapping.
      2. Selecting and coloring an arbitrary range of residues (see example in box at right).
      3. Gaps in the model (2ACE, cf. FirstGlance in Jmol).

    13. Explore Your Molecule
    Day 3, Afternoon 13:00-16:10, Wednesday May 30. Nanobiology Seminar Room 3F.
        Bioinformatics Tools, by Katsumi Imada.

    Day 4, Morning 10:30-12:00, Thursday May 31. Nanobiology Seminar Room 3F.
        Introduction to Multiple Sequence Alignment (MSA) and Conservation
        MSA3D in Protein Explorer
        ConSurf Server
        Membrane Proteins
    1. PE's MSA3D (via PE Site Map, Advanced Explorer): Introduction to multiple sequence alignments.
      1. MSA for 4ENL in black and white (printed handout).
      2. Detail of MSA with color

    2. Identifying Functional Sites & Seeing Protein Evolution:
      1. ConSurf Mechanism.
      2. ConSurf results for 4ENL 50 sequences, 200 sequences, (enolase from Saccharomyces cerevisiae).
      3. ConSurf result from influenze hemagglutinin (in ConSurf GALLERY).
      4. ConSurf Server for Job Submission:
        • ConSurf is under "More Views.." in FirstGlance in Jmol.
        • ConSurf is under "PE Site Map", then "External Resources" in Protein Explorer.

    3. Orientations of Proteins in Membranes.
      1. E. coli Porin 1HXX (beta transmembrane; an outer membrane passive channel for small molecules, also in mitochondria).
      2. "Jmol" link actually goes to FirstGlance in Jmol.
      3. View hydrophobicity.
      4. Compare with hydrophobicity of a soluble protein, e.g. hemoglobin.
    Day 4, Afternoon, 14:40-17:50 Thursday May 31. Computer Lab, GSE Common 2F.
        Seeing Evolutionary Conservation: ConSurf
        Publication Quality Images Easily
        Advanced Protein Explorer


    This afternoon, continue in Windows ME (virtual machine under linux) for compatibility with Chime and Protein Explorer.
    Today we will spend some time answering questions ("challenges") about structures. Use either FirstGlance in Jmol or Protein Explorer, whichever gives the answer more easily.
      Animation from Polyview-3D.
      Click on the above image for
      a larger view and explanation.
    1. ConSurf: Submit your molecule to the ConSurf Server:
      1. FirstGlance in Jmol: ConSurf is under "More Views..".
      2. Protein Explorer: ConSurf is under "PE Site Map", then "External Resources".
      3. Bookmark your ConSurf results page.
      4. FirstGlance in Jmol: Save a snapshot of your results. Paste it into a slide (such as Powerpoint).
      5. Protein Explorer: Save a MolSlide of your results.

    2. Generate publication quality images easily with Polyview-3D.
      1. PyMol: popular with crystallographers. Beautiful views but not user friendly.
      2. Example (at right): 1d66 with Gal4's recognition of the CGG sequence in the DNA highlighted.
      3. Create a rotating view of your molecule, and paste it into a slide (as in Powerpoint).

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

    5. 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.

    6. Challenges. (The challenge questions will be given during class. They are not on-line.)
    Day 5, Afternoon 13:00-16:10, Friday June 1. Computer Lab, GSE Common 2F.
        Mr. Suwa, Life Science Library

    Day 6, Morning 10:30-12:00, Monday June 4. Nanobiology Seminar Room 3F.
        Flagellar Assembly
        Specific Oligomers vs. Crystal Contacts
        Animations and Morphing

      Model of SV40

    1. Introduction to bacterial flagellar assembly: Movie
    2. Specific Oligomers vs. Crystal Contacts
    3. Animations & Morphing
      1. Click "Animations" at PE's FrontDoor.
      2. Animation of NMR ensembles of models to simulate thermal motion
      3. Morphing conformational changes
        • Rationale: Protein Morpher (requires Netscape 4)
        • Lac repressor bending the DNA operon.
      4. Animation of ligand binding (HIV protease inhibitor; protein bending DNA)
    Day 6, Afternoon, 14:40-17:50, Monday June 4. Computer Lab, GSE Common 2F.
        Resources for Teachers


    This afternoon, continue in Windows ME (virtual machine under linux) for compatibility with Chime and Protein Explorer.
    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. (The challenge questions will be given during class. They are not on-line.)

    2. Some challenges may involve Bacterial Flagellar Structures

    3. Calculate isoelectric point (pI) and charge at pH 7. (Get sequence from the Protein Data Bank. Search for PDB code, then use Sequences tab.)

      For Teachers and Future Teachers

    4. BioMolecular Explorer 3D (for students ages 15-19). All Jmol!

    5. Bird Flu: N1 vs. Tamiflu Lesson Plan:
      1. Lecture Slide
      2. Plan for Computer Lab

    6. MolviZ.Org
      1. DNA, Hemoglobin, Antibody, MHC
      2. Lipid Bilayers and Gramicidin Channel
      3. Amino Acid Quizzer
      4. IR Spectra with animated vibrations
      5. Toobers in Science Education

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

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

    9. Building a web page with hyperlinks to Protein Explorer that shows molecules for your teaching or research. Instructions.

    Keep in touch!