Macromolecular 3D Structure Visualization & Structural Bioinformatics
This document is on-line: At proteinexplorer.org click on Workshops, or
Amherst College, Amherst MA USA
Webster 102 Technology Classroom
9:00 AM - 12:30 PM, 1:30 PM - 5:00 PM, Saturday March 10, 2007.
Thanks to Richard Goldsby for initiating this course, and to
Colleen Keenan for IT support.
Main author of FirstGlance in Jmol and Protein Explorer - Prof. Emeritus, Univ. Mass. Amherst; email@example.com
Frieda S. Reichsman
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
introduce participants to finding published macromolecular structure data, and visualizing
and interpreting 3D macromolecular structure using state of the art, free
Structural bioinformatics servers will be introduced that yield
a wide range of
types of key information, yet are easy to use.
Authoring tools that facilitate preparation of interactive macromolecular structure
presentations, such as those at
MolSlides.Org, will be demonstrated.
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
Operates on-line only.
Assumes that you are already familiar with basic principles of protein structure.
Exceptional ease of use. Limited set of "canned" views.
Adopted by Nature
Structural and Molecular Biology and other
Built upon the free, open source Jmol java applet.
Protein Explorer in Chime
and Chime plugin
Operation limited to Windows
Intel Mac OS X).
Operates on-line or off-line (downloaded).
Much more powerful than FirstGlance: fully customizable images
Extensive help and reference materials useful to both students
and researchers. Helps you understand and interpret.
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
Built upon 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
Molecular Visualization Software:
In Web Browsers:
- Jmol java applet (nothing to install except
java, works in all popular browsers, Windows & Mac OS X):
How to Use Jmol.
Sites Using Jmol (growing rapidly!)
Free, open source.
User interface "wrapper": FirstGlance in Jmol:
Free, open source.
- Chime browser plugin (Windows only!
How to Use Chime.
Free, proprietary source, development stalled since 1998.
User interface "wrapper": Protein Explorer (requires Chime):
Free, open source.
Popular with crystallographers because of its power
and gorgeous publication-quality images.
User friendliness: poor.
Documentation: not up to date.
Not free (except for teaching); open source.
- RasMol: Best available from 1993-1997 and still widely used.
User friendliness: poor
(but see user interface
Free and open source.
- DeepView also known as Swiss PDB-Viewer:
Powerful modeling capabilities
(see Molecular Modeling below).
User friendliness: poor.
Free but proprietary source.
- Protein Workshop
(java applet, visualization option at the
Protein Data Bank):
Beautiful images, slow performance.
Ease of use: moderate.
Documentation: so so.
- Many others:
Comparison of Protein Explorer, Cn3D, DeepView:
Review of Protein Chemistry and Structure.
- Central Dogma:
DNA mRNA Protein.
DNA structure in Jmol
- 20 Amino acids
- Codon = 3 nucleotides; 4 nucleotides3 =
- Polypeptide chain geometry and steric restrictions
- Covalent and non-covalent chemical bonds
- 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 in proteins)
- Cation-pi orbital interactions (up to 6.0 Å in proteins)
- van der Waals interactions (up to 4.5 Å in proteins)
- Secondary Structure
- Folding: hydrophobic collapse
- Protein folds cannot be reliably predicted from theory
FirstGlance in Jmol for Simple Visualization
- At firstglance.jmol.org,
enter 1PGB (a
Protein Data Bank identification code). Try these controls:
- Top 2 rows of views
- Center Atom
- More Views
- Cation-pi interactions and salt bridges (1AXI, 1M4U PQS for inter-chain)
- Color by uncertainty
- Explore 1HHO in firstglance.jmol.org,
- Ligands button
- for full names of ligands
- Find (explain the distributions of gly, pro, ala, glu, phe,
viewed one at a time)
- Contacts to HEM
- 1BKX: More Views, Non-standard amino acids
Introduction to Structural Bioinformatics
- 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?
Finding published molecules of interest:
- Browsing Molecules
- Searching for Molecules
Structural Bioinformatics Servers with High Value and Ease of Use:
- Identifying Functional Sites & Seeing Protein Evolution:
Orientations of Proteins in Membranes.
E. coli Porin 1HXX
All-Atom Contact Analysis
(clash scores with hydrogens, model quality):
Generate publication quality images easily with
Save any molecule you see!
- Jmol: click on Jmol, then top item on menu, then bottom item on submenu.
- Chime: click on MDL, then File, then Save Molecule As.
- Upload saved molecule (PDB file) to
Jmol in Scientific Journals:
- FirstGlance in Jmol:
Nature Structural and Molecular Biology
- "Jmolized" Figures:
ACS Chemical Biology
Protein Explorer (more help for beginners than FirstGlance) & MolSlides:
Use Firefox (or Netscape 7.2 or Mozilla).
Go to ProteinExplorer.Org
Internet Explorer cannot save MolSlides, and usually
cannot display the Features of the Molecule control panel
in Protein Explorer.
Netscape 4.8 cannot save MolSlides,
but does everything else in Protein Explorer,
and it works with older Chime-based websites.
Netscape 8 does not work with Protein Explorer.
- Protein Explorer
(8 years of Eric's work!)
- FrontDoor (About Protein)
- FirstView (explanation of backbone traces, ...)
- Features of the Molecule (1E3Q): Resolution, R, Rfree
- QuickViews for Custom Views
- What Are MolSlides?
View MolSlide Examples:
- Demonstration: Making MolSlides in Jmol
- Importing and Adapting MolSlides
BioMolecular Explorer 3D: Molecules for High School
MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.
Bird Flu: N1 vs. Tamiflu Lesson Plan:
MolVisIndex.Org: World Index of Molecular Visualization Resources
- Includes Tutorials, K-12 Resources, Spanish Resources, and many more.
Animations / Morphs: Conformational Changes
Molecular Modeling (Time Permitting, or Later Private Sessions)
- Mutating your model:
Changing residue sidechains and rotamer minimization with DeepView
- DeepView beginners should start with the superb
Molecular Modeling for Beginners
by Gale Rhodes, Univ. Southern Maine.
- DeepView resources are indexed at
- Aligning two or more chains or molecules, and how to view the alignment.
- The CE site
will align any two protein chains quickly and easily
(but hetero atoms are discarded, and its database has not been updated since 2001).
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.
- Homology (comparative) modeling:
Keep in touch!