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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.

  • A one-semester biochemistry course enrolling 40-45 students at Amherst College, Amherst, Massachusetts, USA[1]. 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.
  • 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.



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.


  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:
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