Proteopedia:News

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This page is for external news reports etc. about Proteopedia. For new pages and capabilities within Proteopedia, please see Proteopedia:What's New.

Contents

Add New Items at the Top of Each Section and Date Them, Please!

News on this page is ordered newest first, oldest last, under each subheading. Please include the month and year at the end of each entry that you add below. Subheadings below Statistics are in alphabetical order.

Statistics

Today, Proteopedia has 5,715 registered users. For more information, please see Proteopedia:About. For the number of pages, page views, edits, etc. please see Special:Statistics. The number of times any page has been viewed is displayed at the bottom of the page.

Publications

  • Sharing macromolecule concepts online with Proteopedia, Jaime Prilusky and Joel L. Sussman. eLife Labs June 2016

Adoptions

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.
  • 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.

Adoptions in College and University Classes

See also Student Projects, Teaching Scenes, Tutorials, and Educators' Pages, and Teaching Strategies Using Proteopedia.

  • Amherst College, Amherst, Massachusetts, USA[1]: A one-semester biochemistry course enrolling 40-45 students. 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.
  • Butler University, Indianapolis, Indiana, USA: Jeremy Johnson, March 2024: Proteopedia has become an essential component of my biochemistry course design and a main medium for teaching students about the intricacies and beauty of protein three-dimensional structure and function. In the first semester, students are introduced to Proteopedia as a resource for exploring protein structure and function by studying the Proteopedia page illustrating the structure and dynamics of HIV protease. In the second semester of biochemistry, Proteopedia becomes a central instructional component, as students transition into applying their protein structure knowledge to complex biochemical systems. During a two-hour computational lab, students develop their own stories relating protein structure and function and build Proteopedia pages around a recent high impact protein structure. The ending output from Proteopedia provides students with a high-quality resource that can be shared with friends, family members, and professional school applications and showcases a clear example of their understanding of how a protein’s structure determines its biological function.
  • Ecole Supérieure de Biotechnologie de Strasbourg, France: User:Bruno Kieffer, March 2024: At Level Bachelor 3, groups of 4-5 students edit a Proteopedia page on a protein of their interest. The process is organised into three steps:
    1. The group submits a letter of intent explaining their project to the tutor.
    2. Upon agreement, the project is conducted during 6 to 8 weeks.
    3. Feedback is provided to the whole class and the most mature pages are encouraged to be published as regular Proteopedia entries.
  • Grandview University, Des Moines, Iowa, USA: Bonnie Hall, March, 2024. Students in CHEM 351 Biochemistry create a Proteopedia sandbox page highlighting protein structure and function relationships based on a current journal article. In CHEM 453 Biochemical Techniques, students use the BASIL curriculum to complete an authentic research project. They then publish their results on a Proteopedia page. After their results are reviewed, their pages are made available to all users of Proteopedia (search term: BASIL).
  • Instituto Biociências, Universidade de São Paulo, Brazil. Luis Netto, March, 2024: Proteopedia has been and is a very valuable tool for the students to apply the knowledge they acquired during their theoretical classes. Particularly, they train to perform structural and functional relationships for the proteins that they are interested as they build the proteopedia pages.
  • Stony Brook University, Stony Brook, New York, USA: Biology 207 taught by Marvin H. O'Neal III. 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.
  • Weizmann Institute of Science, Rehovot, ISRAEL:

Press

Blogs

Press Release Re-Posts

Abstract Re-Posts

Miscellaneous Postings

Talks in Meetings and Seminars

Training Workshops

  • 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.

References

  1. ↑ 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
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