Practical Macromolecular 3D Structure Visualization & Structural Bioinformatics
A One-Day Workshop --
Osaka University, Japan
Friday, May 9, 2014, 9:00 - 17:00, Nanobiology Building, Room 308.
Bringing A Laptop Computer Is Encouraged
Host and Co-Instructor:
Thanks to Tohru Minamino and Kana Moriya Nishimura.
, Ph.D.: Lead Instructor.
Principal author of FirstGlance in Jmol; co-developer of Proteopedia and the ConSurf Server.
Professor Emeritus, University of Massachusetts, Amherst --
This document is on-line:
Objectives: Participants will use highly user-friendly
software for visual investigation of 3D molecular structures of
proteins, nucleic acids, and their interactions with each other
and with ligands, substrates, and drugs; and of protein evolutionary
conservation. Hands-on experience will be largely with molecules
of each participant's choosing. Participants will learn how to
create publication-quality molecular images, rotating molecules
in Powerpoint slides, and custom on-line rotating molecular
scenes in Jmol.
All software in this course is free, and works on Windows, Mac OS X, or linux.
Level & Pace: This workshop is designed for faculty, postdocs,
research staff and graduate students
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
- Installing and Enabling Java
You can see molecules without Java, using
in the two main tools
of this course:
For most other sites that display molecules in Jmol, you will need to
install and enable Java.
Java will also make Proteopedia and FirstGlance run faster and smoother.
In this course, we will use all 3 forms of Jmol that work in web browsers:
four forms of Jmol.
- JSmol (no Java)
- Jmol_S (signed Java applet)
- Jmol (unsigned Java applet,
instructions for installing/updating and enabling Java.
- TA's and Instructors will help you!
- Can you see this
Gal4:DNA complex with Java
- If you got Java to work, use the Preferences tab in
FirstGlance to make Java the default. Then
this link to Gal4:DNA
should use Java
- Some sites use an older, unsigned
Java applet. An example
is this explanation of
Protein Secondary Structure. Can you see the molecule?
Make sure to
Enable Unsigned Java Applets
for this website. Later in the course, you may want to enable other
Get Started Individually At Proteopedia
Before we start the next section together, while the group is getting organized ...
- Go to
Proteopedia.Org and take a look around.
- Try searching for some of your favorite molecules.
Workshop Overview (Powerpoint Slides)
Proteopedia.Org Part I
Protein Data Bank & PDB Codes
The Protein Data Bank (PDB) --
World Wide: -- USA:RCSB -- Japan:PDBj -- Europe:PDBe
PDB identification code examples:
- 1hho oxy-hemoglobin.
- 1d66 Gal4 transcriptional regulator bound to DNA.
- 104d DNA/RNA hybrid.
- 1bl8 potassium channel.
- 91ns insulin.
- Main page: green links connect text to molecular scenes.
- Molecules explained by users. Example:
- Random articles or molecules.
- Identify by touching (shows a "hovering" report).
- Pop up any molecular scene.
- Save any page for off-line projection.
- Explanations of structural biology terms and concepts, e.g.
asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value,
etc. all at
About Macromolecular Structure.
- Pages in
Japanese, Chinese, Arabic, Turkish, Russian, etc.
- Has a page for each of the >90,000 PDB entries, showing it in Jmol.
- Title and Abstract.
- Shows resolution (see
- Link to FirstGlance in Jmol on every PDB code page.
- X-Ray Crystallography and Resolution
Finding published molecules of interest
Each participant should find a molecule of personal interest.
- Searching for Molecules
Get the amino acid sequence of your protein. You could find it in
Use the sequence
of your protein to search for 3D structures.
Write down the
- At pdb.org,
click Advanced Search. Choose the Query type
"Sequence Features: Sequence". Paste your sequence in the large box and
click Submit Query.
Powerful but sometimes difficult to use; help is sometimes inadequate.
Offers the most detailed information about hits.
Useful short summaries of hits.
Powerful and straightforward.
Useful results table.
- PDB-Japan Sequence Navigator
Not for sequence searching, but sometimes useful.
- Can't find an empirical 3D model for your sequence?
- Browsing Molecules: Good places for students to choose molecules for class assignments.
Review of Protein Chemistry and Structure.
We'll do this quickly. The links are for participants who are educators.
- Central Dogma:
DNA mRNA Protein.
DNA structure in Jmol
Estructura del ADN
- 20 Amino acids
Polypeptide chain geometry and steric restrictions
Covalent and non-covalent chemical bonds
- Codon = 3 nucleotides; 4 nucleotides3 =
Typical hydrogen bond
within a protein: hydrogen donor atom
is covalently bonded to hydrogen; acceptor
atom is not. In proteins, donor-acceptor distance
can be 2.5 to 3.5 Å.
Folding: hydrophobic collapse
cannot be reliably predicted
from sequence alone (using ab initio theory).
- Covalent bonds: lengths and angles nearly constant
- Non-covalent bonds: variable lengths and angles
- Salt bridges (up to 4.0 Å in proteins)
Hydrogen bonds (2.5-3.5 Å donor-to-acceptor in proteins)
Cation-pi interactions (up to 6.0 Å in proteins)
- van der Waals interactions (up to 4.0 Å in proteins)
Evolutionary Conservation: ConSurfDB & ConSurf
Major histocompatibility protein (MHC I 2VAA):
Identifying Functional Sites & Seeing Protein Evolution:
- At 2vaa in
show Evolutionary Conservation.
- Also check
(cathepsin B, noting the conserved surface Gly, Pro --
- ConSurf's Mechanism:
- Note the Caveats in
Proteopedia's Evolutionary Conservation.
- There are two ConSurf Servers:
- Pre-calculated for every chain in the PDB.
- Results are shown in Proteopedia.
- Multiple Sequence Alignments typically include proteins of
more than one function, so some conservation may be hidden.
- Set up each job by hand.
- Easily select sequences for a single protein function, revealing
conservation (within a family of proteins performing
a single function) that may be hidden in ConSurfDB.
- If you have a serious interest in the conservation in your protein,
FirstGlance in Jmol: Easy Visualization of Any Macromolecule
Terminology: "visualization" vs. "modeling".
(Light modeling tools)
- There are two ways to get FirstGlance:
- Go to
Proteopedia.Org, enter the PDB code in the search slot.
Below the molecule, under
Resources, click on the link
- Go to
FirstGlance.Jmol.Org and enter the PDB code.
(Or go directly to
- Preferences are independent. If you want to use Java, you need
to set that preference at BOTH sites.
- Explore 1izh in FirstGlance.
- Molecule tab
- Year, Method.
- Free R
- Chain details.
- Sequences: Crystallized vs. Full Length. Alignment at UniProt
- Text contents of the PDB file.
- Views tab
- Top 3 rows of views:
Secondary Structure / Cartoon / N->C Rainbow
Composition / Hydrophobic/Polar / Charge..
/ Vines / Thin Backbone
Ligands+ / Water / Slab
Hydrophobic core: Hydrophobic/Polar, then Slab.
Amphipathic helices and strands. (In FirstGlance,
Hide a range (the helix or strand) then invert.)
- Compare with
- Resources tab
- See lipid bilayer boundaries.
Tools tab with Views.
- Salt bridges.
- Salt bridges in Charge View.
- Charges with Slab on.
- Sidechain distributions in Vines View.
- Find (review Chart of AA): PHE, (VAL,LEU,ILE), ASN, THR
- Explore 2mcg in FirstGlance.
- Tools tab
- Explore 3onz in FirstGlance. (Letter O not numeral zero!)
- Molecule tab
- Two chains, not sequence identical.
- Missing residues.
- Ligands+ and non-standard residues
- Views tab
- Ligands button; smaller ligands.
- Hide (chain, toluene, isolated His).
- Non-covalent interactions for HEM in chain A (blue chain).
- Resources tab
- Biological unit.
Introduction to Structural Bioinformatics and Genomics
Educators: You are welcome to use the slides linked below, or to adapt content from them into your own slides.
- Slides Covering:
- Why do we care about 3D macromolecular structure?
- What are 3D structure data?
- Where do 3D structure data come from?
- How much 3D structure knowledge do we have?
- What are the primary and derived 3D structure databases?
Proteopedia.Org (Part II): Authoring
- Add Molecular Scenes and Content to
- Its a wiki: you or your students can add pages or customized
molecular scenes in Jmol.
- Great for
journal supplementary materials
research group websites
as well as
molecular structure tutorials
your pages from
being changed by anyone else, e.g.
- An easy Scene Authoring Tool attaches your customized
views to Green links.
- This is, by far, the easiest place to create molecular tutorials,
Nucleosomes (publically editable).
(enough for your entire class!) allow students to try
authoring temporary molecular scenes -- without individual accounts.
Screenshots can document student work.
Teaching Strategies Using Proteopedia.
Animated Powerpoint Slides and Publication-Quality Images:
from Polyview-3D. Click on
the image for a
larger view and explanation.
Make Animated PowerPoint Slides and Publication-Quality
Images easily with
- Just fill out an easy form, submit it, and (shortly) voila!
Center and orient the molecule as you wish.
Coloring can be customized. Highlight residues that you specify.
Accepts PDB files obtained from ConSurf to color your figures or
slides by evolutionary conservation.
Once you have an animation from Polyview-3D:
- Windows Powerpoint: Simply drag the animation directly from the
Polyview-3D web page and drop it into a powerpoint slide.
- Mac OS X Powerpoint: (This works in Powerpoint:Mac 2008.)
Control-Click (Right-Click) on the animation in the Polyview-3D web page, and
select Save Image As ...
Save the image to the Desktop.
- Drag the image file (filename ending in .gif) from the Desktop and
drop it into a Powerpoint slide.
The animation will run only when the slide is projected.
We won't have time to go through the following resources in detail, so
the links and information below are provided mostly for you to use, if you wish, after the workshop.
Potassium channel (1R3J) showing membrane surface planes
- FirstGlance -> Resources Tab:
Orientations of Proteins in Membranes.
Jmol in Scientific Journals:
Interactive 3D Complements in Proteopedia:
- FirstGlance in Jmol: Look for the 3D View links
Nature Structural and Molecular Biology
- "Jmolized" Interactive 3D Journal Figures:
- Tutorials disponible en español at
MolviZ.Org (Estructura del ADN; Modelo de bicapa
lipídica y canal de gramicidina; Estructura del agua:
enlaces de hidrógeno)
BioModel (Estructura de proteínas; Glúcidos,
Lípidos, Vitaminas, Aminoácidos, Hélice alfa,
Hebra beta, Lisozima, Nucleósidos, ADN, ARN, et al.)
HighSchool.MolviZ.Org: Resources for High School Teachers.
- BioMolecular Explorer 3D: Molecules for High School.
- Molecular Workbench (from Concord Consortium):
Activities for High School Students with built-in assessment and reporting.
If this image is not moving, reload the page!
Morph of the lactose repressor bending DNA as it recognizes
Teaching Scenes, Tutorials, and Educators' Pages in Proteopedia, including Molecule of the Month.
- Teaching Strategies Using Proteopedia.
MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.
- Bird Flu: N1 vs. Tamiflu Lesson Plan:
Animations / Morphs: Conformational Changes
(see MOVIE at right).
- Mutating your model:
Changing residue sidechains and rotamer minimization with
- DeepView beginners should start with the superb
Molecular Modeling for Beginners
by Gale Rhodes, Univ. Southern Maine.
- DeepView resources are indexed at
- Structural Alignment of two or more chains or molecules, and how to view the alignment.
can align macromolecules
(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 Jmol can distinguish the models.
Gale Rhodes provides a
DeepView tutorial: click on the section Comparing Proteins.
Structural Alignment Tools.
- Homology (comparative) modeling:
Keep in touch!