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- Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
- Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules, Jaime Prilusky, Eran Hodis, David Canner, Wayne A. Decatur, Karl Oberholser, Eric Martz, Alexander Berchanski, Michal Harel and Joel L. Sussman. Journal of Structural Biology 175:244-52, August 2011 or doi:10.1016/j.jsb.2011.04.011.
Adoptions by Structural Bioinformatics Resources
Some bioinformatics databases and resources have adopted Proteopedia. This means that they have chosen to offer links to Proteopedia for the benefit of their users.
- ExPASy Proteomics Server (EXpert Protein Analysis SYstem) of the Swiss Institute of Bioinformatics offers links to Proteopedia on its 3D structure pages, e.g. PDB code: 1A5H. October, 2008.
- TOPSAN, The Open Protein Structure Annotation Network, a wiki designed to collect, share and distribute information about protein three-dimensional structures. October, 2008.
- Protein Crystallography Universe, a website provided by Rigaku Life Sciences Group, links Proteopedia under Structure Analysis and Reference Shelf. October, 2008.
- CATH, a hierarchical classification of protein domain structures [Class (C), Architecture (A), Topology (T) and Homologous superfamily (H)], provides links on its PDB pages to Proteopedia. September, 2008.
- GeneCards, a searchable, integrated database providing concise information on all known and predicted human genes, links relevant proteins to Proteopedia. September, 2008.
- Jmol Tutorial-Authoring Template (JTAT) automatically provides a link to Proteopedia for each PDB file illustrated in its tutorials. August, 2008. See, for example, the bottom right (Explore further ... under How To ...) in the JTAT Demo Tutorial.
- Molecule of the Month by David S. Goodsell provides links to Proteopedia in some recent articles. An example is linked at the end of the second page of the article on Selenocysteine Synthase. August, 2008. Here is the complete list.
- OCA Database and Browser for 3D macromolecular structure has a link from each PDB entry to Proteopedia. August, 2008.
- PDBsum has a link to Proteopedia on every PDB entry page. August, 2008.
- PDBWiki has a link to Proteopedia on every PDB entry page. August, 2008.
- RCSB Protein Data Bank (see Proteopedia's page on the Protein Data Bank), has a link from each PDB entry to Proteopedia, but it can be a bit hard to find. To find it: At the Structure Summary tab/page for a given PDB code, in the menu at left, click on External LInks. On that page, you'll find a link to Proteopedia under Structure Summary. If you think it would be useful to have a more prominent link to Proteopedia at RCSB-PDB, please email . In May, 2008, an international group of several structural bioinformaticians and crystallographers requested that a link to Proteopedia replace the present Jmol link under Display Options at the upper right of the main Structure Summary page for each entry, but that request was denied. Eric Martz 03:19, 7 August 2008 (IDT)
- Pfam, a large database of protein families, each represented by multiple sequence alignments and hidden Markov models, will offer links to Proteopedia beginning with Pfam release 23. August, 2008.
- PSI Structural Genomics Knowledge Base has a link to Proteopedia, on its Annotations tab, for every PDB entry. August, 2008.
Adoptions in College and University Classes
- A one-semester biochemistry course enrolling 40-45 students at Amherst College, Amherst, Massachusetts, USA. Several professors introduce students to Proteopedia and FirstGlance in Jmol in laboratory, use them in lectures, require molecular images in homework tasks, and require their use in a structure-function analysis capstone project and a presentation of their results. February, 2014.
- Advanced Molecular Biology (Biochem 642, for graduate students) taught by Drs. Robert Zimmermann and Alice Cheung at the University of Massachusetts, Amherst, Massachusetts, USA. A two-session, hands-on workshop introducing First Glance in Jmol and Proteopedia's Scene authoring tools was taught by User:Wayne Decatur, who prepared Biochem642 Molecular Visualization Sessions and Teaching Proteopedia. Students were assigned problem sets that required authoring accompanying scenes in sandbox pages. November, 2009.
- Biomolecular Structure (Chem 791a, for graduate students) taught by crystallographer Jeanne Hardy at the University of Massachusetts, Amherst, Massachusetts, USA. A computer lab workshop introducing the Scene authoring tools was taught by User:Wayne Decatur, who prepared Chem791A Work Session and Teaching Proteopedia. November, 2008.
- Biology 207 taught by Marvin H. O'Neal III at Stony Brook University, Stony Brook, New York, USA. Students work in groups of 2-4 to create a Proteopedia Workbench page. The Workbenches mechanism is used because it keeps the student project in one student's User: space (which protects the page), and enables collaboration by using the workbench tab to permit other members of the group, and the instructors, read/write access.
- CBI_Molecules has involved a number students at the University of Massachusetts at Amherst, Massachusetts, USA producing excellent pages for display on the Molecular Playground. Professor Lynmarie K. Thompson who has been involved with this has used Proteopedia for student projects in Chemistry 423 in 2011 and 2012.
- PDB Education Corner, Winter 2011
- GENnews Best Of The Web: Proteopedia , May, 2010
- The Scientist: "Structure Made Simple". March, 2010
- Seed Magazine: "Scientific Truth in the Age of Wikipedia". February, 2009
- Proteopedia in Faculty of 1000. October, 2008
- Nature Reviews Molecular Cell Biology - October, 2008 Research highlights
- Nature Cell Biology - October, 2008, Proteopedia mentioned in Editorial
- GenomeBiology.com Press Release August, 2008
- edfed Proteopedia collects and disseminates information about molecules, February 8th, 2010
- Molecular Modeling Basics October, 2009. A blog related to the book of the same name.
- BeckerInfo.net Open Source Visualization December, 2008
- http:// car54.wordpress.com August, 2008 (Web site not longer available)
- Wonder: Sci-Tech Department August 2008
- The Scientist -- Richard Grant's blog on Nature Network March 2008
- Peter Murray Rust's blog March, 2008
Press Release Re-Posts
- mechanical engineering November, 2008
- Science Daily August, 2008
- The Wired Campus August, 2008
- e! Science News August, 2008
- Medical Health Articles August, 2008
- YAHOO! News, India August, 2008
- Proteopedia – pierwsza encyklopedia z trójwymiarową zawartością August, 2008
- WEBINDIA123 August, 2008
- pda.physorg.com August, 2008
- Europe Sun August, 2008
- AECC August, 2008
- AlphaGalileo August, 2008
- Bio-Medicine August, 2008
- FEEDZILLA August, 2008
- EurekAlert! August, 2008
- FirstScience News August, 2008
- Latest News August, 2008
- ICONOCAST August, 2008
- ICONOCAST Spanish August, 2008
- PHYSORG.com August, 2008
- Science Codex August, 2008
- www.scientificblogging.com August, 2008
- Thaindian News August, 2008
- polit.ru August, 2008
- infuture.ru August, 2008
- The Smart Techie August, 2008
- Scientific texts in 3D with interactive formats developed Silicon India August, 2008
- Scientific texts in 3D with interactive formats developed newKerala.com August, 2008
- 3D interactive text formats developed, NDTV.com August, 2008
- innovations report August, 2008
- Medical News Today August, 2008
- Online wiki hosts interactive, 3D molecular structures, iTnews August, 2008
- Scientific texts in 3D with interactive formats developed, SiFy news August, 2008
- Nominated for Best Website in the Labbies Awards by the TheScientist.com June, 2010
- digg.com/tech_news digg/Tech News August, 2008
- StumbleUpon August, 2008
- TIEDE.fi August, 2008
Talks in Meetings and Seminars
- Proteopedia - a Scientific 'Wiki' Bridging the Rift Between 3D Structure and Function of Biomacromolecules, HUGO's 13th Human Genome Meeting, September, 2008.
- In I am not a PDBid I am a Biological Macromolecule, the keynote talk at 3DSig 2008, Structural Bioinformatics and Computational Biophysics (an ISMB satellite meeting Toronto, 18-19 July 2008), Philip E. Bourne discussed removing the barrier between the literature and the PDB, featuring his BioLit project. In this context, he listed Proteopedia as Possibility 1, "a completely new beginning", and discussed its advantages (anyone can contribute leading to wiki quality) and disadvantages (reward for authoring? limitations of wiki format).
- Short courses and one-day workshops are taught by Eric Martz on macromolecular structure visualization and structural bioinformatics. These now include a segment on Proteopedia, including use of Proteopedia's Scene-Authoring Tools. In 2008, these have been at the Weizmann Institute of Science in Israel, and at Osaka University and the Okinawa Institute of Science and Technology in Japan. For curricula and upcoming dates, please see Workshops.MolviZ.Org. August, 2008.
- ↑ Jaswal SS, O'Hara PB, Williamson PL, Springer AL. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course. Biochem Mol Biol Educ. 2013 Sep-Oct;41(5):351-9. doi: 10.1002/bmb.20718. Epub, 2013 Sep 10. PMID:24019219 doi:http://dx.doi.org/10.1002/bmb.20718