Adoptions
The following bioinformatics resources use FirstGlance in Jmol
to display specific molecules. Most simply link
to http://firstglance.jmol.org, thereby avoiding the need to install
FirstGlance on their own servers. Those designated
Mirror Sites
have installed FirstGlance
on their own servers.
Journals
- ACS Chemical Biology, a journal from the
American Chemical Society,
began offering interactive 3D figures (crafted in Jmol by
Frieda Reichsman/MoleculesInMotion.Com)
in December, 2006. Each such figure has links to FirstGlance in
Jmol. The first paper with such figures concerned the
structure of an HIV reverse transcriptase complex with an inhibitor
by Himmel et al. (go to a figure and click on "3D interactive version").
- Molecular
Biosystems, a journal from the
Royal Society of Chemistry (London, UK).
Founded in 2005, its focus is
"on the interface between chemistry and the -omic sciences and systems biology".
Links to FirstGlance in Jmol debuted in June, 2006. See
Molecular BioSystems moves into a new dimension,
and
3D View adds a new dimension.
- Nature,
a weekly international journal founded in 1869 with editorial
offices in London, Europe, USA, and Asia. Nature is one of
the world's
highest impact
scientific journals, and is the
most cited weekly science journal.
(According to the
Top 100 Journals Reporting Macromolecular Structures, it
ranks tenth in published quantity of entries in the Protein Data Bank.)
FirstGlance in Jmol debuted in the November 30, 2007 issue
(see the "3D View" links). In the September 23, 2010 issue, Nature ceased having
direct 3D View links to FirstGlance in Jmol.
- Nature Structural and Molecular
Biology, a
monthly journal with editorial headquarters in New York (NY, USA),
reporting
newly solved macromolecular structures.
(According to the
Top 100 Journals Reporting Macromolecular Structures, it
ranks seventh in published quantity of entries in the Protein Data Bank.)
FirstGlance in Jmol debuted in the February, 2006 issue accompanied by
We're living in a 3D world.
See the "3D View" links (which continue as of January, 2013).
- Protein
Science announced the adoption of FirstGlance in Jmol
in 2009: Interactive graphics return to Protein Science.
Every
PDB code mentioned is linked to FirstGlance in Jmol
(look for "PDBid" next to such links in the text of an article).
See also
Jmolized Figures.
This journal pioneered
interactive 3D figures
(now done with Jmol in
several journals including Protein Science)
in the 1990's, using
Kinemages.
Structural Bioinformatics Servers & Databases
- ConSurf Server from
Tel-Aviv University (Israel). Colors 3D protein structures by evolutionary
conservation, facilitating the identification of functional surface
patches. ConSurf offered visualization in Protein Explorer since its
inception (fall 2001), and added FirstGlance in Jmol in September, 2006.
- ExPASy (EXpert
Protein Analysis SYstem) of the Swiss Institute of Bioinformatics has links to FirstGlance
in Jmol from its 3D structure pages, e.g.
Tamiflu-resistant influenza neuraminidase (3ckz).
- Membrane
Protein Data Bank from Ohio State University (Columbus, Ohio, USA).
Powerful search capabilities for integral, peripheral, and anchored membrane
proteins, with stastics including total, unrelated, and families.
FirstGlance in Jmol was added about February, 2006.
- OCA,
a browser-database for protein structure/function
from Bioinformatics and Biological
Computing of the
Weizmann Institute of Science
(Rehovot, Israel).
OCA provides
a powerful search interface to the Protein Data Bank, as well as
PDB
Lite for beginners.
OCA provides Mirror Sites for FirstGlance in Jmol
on several continents beginning in November, 2005.
- Orientations of Proteins
in Membranes (OPM) database from the University of Michigan
(Ann Arbor, Michigan, USA).
OPM provides visualization of hydrophobic thicknesses,
and orientations of membrane
proteins with respect to the hydrocarbon core of the lipid bilayer,
by adding planes of pseudo-atoms to the PDB file, representing
the surfaces of the lipid bilayer. Visualization in FirstGlance in Jmol
has been offered since December, 2005.
- PDBWiki from the Structural Proteomics
Group at the Max-Planck-Institute for Molecular Genetics (Berlin, Germany).
- Pepitope Server from
Tel-Aviv University (Israel). Predicts epitopes, including discontinuous
epitopes, on the surfaces of protein antigens of known 3D structure, given
one or more peptides that bind to an antibody. FirstGlance in Jmol was
incorporated at the inception of this server, about December 2006.
- Probable
Quaternary Structure (PQS) server
of the
European Bioinformatics Institute (Hinxton, UK).
This unique server provides coordinates for specific oligomers,
or monomers (when multiple copies in the crystallographic asymmetric unit
result from crystal contacts).
More. PQS has offered links to FirstGlance in Jmol since
February, 2006.
Also, PQS is linked within FirstGlance in Jmol with a prominent "PQS" button.
-
Protein Data Bank USA (a branch of the
World Wide Protein Data Bank), the central repository
for all published, empirical, macromolecular 3D structure data.
Began offering links to FirstGlance in Jmol about September, 2007.
Under the molecular image at the upper right, select Asymmetric Unit.
Then you will find FirstGlance on the Other Viewers menu
below the molecular image. Note that the View in Jmol is NOT
FirstGlance in Jmol. Also note that Biological Assemblies
do not offer FirstGlance in Jmol, which would generally not be
useful anyway because symmetry-related chains all have the same name,
and are in different models.
See
Biological Unit.
- Proteopedia from
the Weizmann Institute of Science (Israel). A wiki with automatically-generated
pages for every published macromolecular structure (the entire PDB) including
the published abstract and views in Jmol including functional sites and ligands,
and a link to FirstGlance in Jmol.
Text contains green links that change the molecular scene in Jmol.
A molecular Scene-Authoring Tool makes it easy to add new molecular
scenes attached to green links in the text.
- Selecton Server from
Tel-Aviv University (Israel).
The ratio of non-synonymous (amino-acid altering) to synonymous
(silent) substitutions, known as the Ka/Ks ratio, is used to
estimate both positive and purifying selection at each amino-acid
site. FirstGlance in Jmol has been offered since the inception of
this server in April, 2007.
- TOPSAN, The Open Protein Structure Annotation
Network, from
the Joint Center for Structural Genomics (California, USA).
A wiki providing detailed information about some of the 3D structures solved by Protein Structure Initiative,
a part of the worldwide structural genomics initiative.
Adaptations
Sites below have made custom modifications to the freely available
source code of FirstGlance in Jmol, adapting it to meet
their needs.
-
ProteinGlimpse is a Macintosh widget "inspired
by FirstGlance in Jmol".
(We recommend using a pop-up blocker when visiting this site.)
-
Ribosomal Modification Maps in 3D at the University
of Massachusetts, Amherst, has adapted FirstGlance in Jmol for their 3D viewer.
-
The
Yeast snoRNA Database at the University
of Massachusetts, Amherst, has adapted FirstGlance in Jmol for their 3D viewer.
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