FirstGlance in Jmol
(firstglance.jmol.org)
enables you to explore any molecule using menus
and buttons, without learning any commands, and
with nothing to install.
It works immediately with all popular browsers and computer types.
It is designed for professionals reading journal articles (look for 3D View
links in Nature
Structural and Molecular Biology, among others).
It has less help for students
than Protein Explorer, but it is simpler to use.
FirstGlance in Jmol offers several one-click preset views,
makes it easy to hide portions of the molecule,
find residues by sequence number or name,
show all protein salt bridges and cation-pi orbital interactions
(under More Views..). Its Contacts.. dialog
shows non-covalent bonds to any
target moiety that you select by clicking, dividing them into seven
categories that you can hide or display with checkboxes.
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ConSurf
output: functional variability of the peptide-binding groove
of MHC I is displayed in 3D in Protein Explorer. |
See evolutionary conservation!
ConSurf makes it easy for you to identify
functional regions of proteins. Each amino acid is colored
by evolutionary conservation, thereby making clear conserved or highly
variable patches.
Results are displayed in
FirstGlance in Jmol
(or
Protein Explorer). Results can be downloaded
in a single
PDB file
and later uploaded to FirstGlance in Jmol for display.
This user-friendly
tool finds related protein sequences,
performs multiple sequence alignments,
constructs a phylogenetic tree,
and assigns a conservation level to each amino acid,
all automatically!
Optionally, you can select the sequences and upload your own
multiple sequence alignment, which will be used by ConSurf's
state-of-the-art algorithms, all of which are published.
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ProteinExplorer.Org
Chime
*Win-IE6-Compatible*
(en
español) Downloadable
With ProteinExplorer.Org
you can explore any molecule, using menus and buttons
without typing any commands. Makes visual exploration of macromolecular
structure much more accessible to novices and research professionals alike.
Easier to use and more powerful than RasMol. And, if you have used RasMol,
you can enter any commands you have already learned.
Includes
Lesson
Plans for Educators. In addition, it's
downloadable
for off-line use!
Reviews: 
Protein
Explorer review by MERLOT. PE received the highest rating and
won the annual
MERLOT Classics Award for 2003:
"Protein Explorer has revolutionized the teaching of biology
at a molecular level."
More reviews.
Learn how to use Protein Explorer quickly and efficiently by
viewing our interactive Flash movie, Getting
Started in Protein Explorer.
Make slides with rotating molecular structures!
PE makes molecular structure slides called MolSlides. See examples
at MolSlides.ProteinExplorer.Org. MolSlides of
any molecular view achieved in PE can be saved with a few clicks of the mouse.
Advance to the next MolSlide by pressing the spacebar.
PE includes a MolSlide Manager for importing sets of MolSlides, merging,
re-organizing, and updating. MolSlides can be presented in Chime or Jmol.
For more information, please see
MolSlides.ProteinExplorer.Org.
Create presentations in PE!
Presentations
in Protein Explorer (PIPEs)
encourage seamless transitions between the author's views of the molecule,
and self-directed exploration using PE's QuickViews toolkit.
Each and every view can be further explored on the spot if desired,
returning to the author's presentation of views whenever appropriate.
Lesson Plans: For peer-reviewed papers on how to use Protein
Explorer in teaching, comments from teachers,
databases that display results in PE, and more, see
Protein Explorer Lesson Plans
and
Protein Explorer Literature.
Also available within Protein Explorer: ready-made slides
Introducing Structural Bioinformatics.
The downside:
Because Protein Explorer requires the free
MDL Chime plugin,
it works only in Windows and best in Firefox.
It works perfectly in
Windows inside Intel Mac OSX.
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Fantastic
Teaching Props
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Toobers in Science Education: Model Your Favorite
Polymer
Toobers
are inexpensive, easy to bend, foam-covered rods that hold the shapes
you give them, over and over again!
They are very useful in illustrating macromolecular structure concepts.
Great for all levels of science from K-12 to undergraduate. We
feature several examples and also short movies to illustrate their use.
Physical
Models of Molecules
Colorful, accurate models featuring embedded magnets
to simulate hydrogen bonding, at varying prices—kits for water,
for assembling DNA from nucleotides (image at right), and other molecules. Available for purchase from
3DMolecularDesigns.com;
several available to local teachers through the Physical
Model Lending Library (Western MA USA only). For information
on how high-precision models are made, see the
Rapid
Prototyping section of
History
of Visualization of Biological Macromolecules.
Physical
Model Lending Library (Western MA only)
 More
than 10 different models are available for short-term loan (about 10 days)
to teachers in Western Massachusetts, including:
- Anthrax protective antigen heptamer
- Antibody bound to lysozyme antigen
- DNA double helix
- Green fluorescent protein
- The nucleosome
- Transfer RNA
- Water with NaCl, EtOH, Ethane
To reserve models, and for more information, see the
Lending
Library for Physical Molecular Models for Western Massachusetts, USA.
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Related Resources
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Make Publication-Quality Molecular Images and
Rotating Powerpoint Slides Easily!
History
of Visualization of Biological Macromolecules
The History
of Visualization of Biological Macromolecules answers questions
such as, Where did MDL 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.
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Feedback to Eric Martz
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and
?
DNA Structure
Hemoglobin
Antibody
Major
Histo- compatibility Complex
Lipid
Bilayers and Membrane Channel
Periodic Table of the Elements
IR Spectrum
at MolviZ.Org?
The
