Adoptions of FirstGlance in Jmol

Adoptions & Adaptations of
FirstGlance in Jmol
Updated January, 2013; July, 2018.

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. (Whether links to FirstGlance in Jmol continue in 2018 has not been determined.)
Nature offered FirstGlance in Jmol for 10 years and 4 months, from 2007 to 2018. Nature is 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 eighth in published quantity of entries in the Protein Data Bank [As of July, 2017].) FirstGlance in Jmol debuted in the November 30, 2007 issue (see the "3D View" links). The on-line format was redesigned starting with the September 23, 2010 issue, and the single structure article in that issue has no link to FirstGlance in Jmol. However, those links, subsequently labeled with a "3D" graphic and the PDB code, were reinstated in the next issue (September 30, 2010), in the section Accession Codes (no longer accessible from the Table of Contents). Links to FirstGlance in Jmol continued through April 5, 2018, but were discontinued starting April 12, 2018.
Nature Chemical Biology, a monthly journal with editorial headquarters in Cambridge MA (USA). Macromolecular structures have been linked ("3D" graphic) to FirstGlance in Jmol since January, 2010. (Whether links to FirstGlance in Jmol continue in 2018 has not been determined.)
Nature Chemistry, a monthly journal with editorial headquarters in London, UK, and Cambridge MA (USA). Macromolecular structures have been linked ("3D View") to FirstGlance in Jmol since September, 2013, and possibly earlier. (Whether links to FirstGlance in Jmol continue in 2018 has not been determined.)
Nature Communications, a monthly journal with editorial headquarters in London, UK, and Shanghai, China.. Macromolecular structures have been linked ("3D" graphic) to FirstGlance in Jmol since July, 2010. (Whether links to FirstGlance in Jmol continue in 2018 has not been determined.)
Nature Reviews Molecular Cell Biology, a monthly journal with editorial headquarters in London, UK. Macromolecular structures have been linked ("3D" graphic) to FirstGlance in Jmol since July, 2013 (or possibly earlier). (Whether links to FirstGlance in Jmol continue in 2018 has not been determined.)
Nature Structural and Molecular Biology provided links to FirstGlance in Jmol for 12 years: 2006-2017. It is 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 eighth in published quantity of entries in the Protein Data Bank [as of July, 2017].) FirstGlance in Jmol debuted in the February, 2006 issue accompanied by We're living in a 3D world. December, 2017 was the last issue offering links to FirstGlance in Jmol.
Protein Science offered links to FirstGlance in Jmol for five years. It announced the adoption of FirstGlance in Jmol in 2009: Interactive graphics return to Protein Science. Every PDB code mentioned was linked to FirstGlance in Jmol (look for "PDBid" next to such links in the text of an article). Five years later, in November, 2014, the links were changed to the RCSB PDB. 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).
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.
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.
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.

Adaptations
Sites below have made custom modifications to the freely available source code of FirstGlance in Jmol, adapting it to meet their needs.

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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