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Welcome to Proteopedia The free, collaborative 3D-encyclopedia of proteins & other molecules ISSN 2310-6301

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Featured Article Green links change the 3D image! Click and drag on the molecule! load='1stp' size='350' scene='User:David_Canner/Sandbox_HIV/Opening/2' spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image HIV-1 protease by David Canner The X-ray structure of HIV-1 protease reveals that it is composed of , each consisting of 99 amino acid residues. The subunits come together in such as way as to . This tunnel is of critical importance because the active site of the protease is located in its interior. The active site consists of , making it a member of the aspartyl protease family. The two Asp's are either interact with the incoming water OR protonate the carbonyl to make the carbon more electrophilic for the incoming . (more...) Previously featured articles... What Can Proteopedia Do For You? Scientists and Students Educators Structural Researchers Understand 3D structure-function relationships Intuitively communicate your favorite 3D structure to a broad audience Develop tutorials or molecular scenes to project during lectures Assign students to construct pages in Proteopedia for class projects or reports Create Interactive 3D Complements for your journal publications Create pages about your research group, highlighting structures of interest to your group (Example: HIV-1_protease - On how drugs combat the Human Immunodeficiency Virus) (You may protect your teaching pages from editing by others.) (You may protect such pages from editing by others or hide them from viewing pre-publication.) Proteopedia News How to display cavities, pockets, and tunnels. November 2024: How To Find A Structure is a new guide to finding an empirical model for a protein of interest, choosing which empirical structure is best, and getting an AlphaFold-predicted structure when no empirical structures are available. November 2024: How to predict structures with AlphaFold has been updated with instructions for the latest AlphaFold3 Server. November 2024: A handful of case studies illustrate what Nobel-Prize winning AlphaFold3 can, and cannot, predict. November 2024: There is a new guide to being aware of, and dealing with missing residues and incomplete sidechains. March 2024: Professors are using Proteopedia for class projects in Brazil, Czech Republic, France, and various states in the USA. See the updated Adoptions in College and University Classes. What happens if a SARS-CoV-2 coronavirus enters your lung? See a clear explanation at Lifecycle of SARS-CoV-2 July 2022: Exercise-induced N-lactoyl-phenylalanine, appetite and obesity 5,000 users!! On December 4, 2021, the number of Proteopedia users went over 5,000. The 5,000th user is from Juniata College, Huntingdon, Pennsylvania, US AlphaFold protein structure predictions - a step change for biology, an electronic talk by EBI staff for students and early career researchers via FEBS Junior Sections, Oct. 26, 2021, 19:00 CEST. Announcement. Registration. A practical guide to teaching with Proteopedia January 2021: How to display cavities, pockets, and tunnels? Jmol/Cavities_pockets_and_tunnels December 2020: What is changing on SARS-CoV-2 virus and what this means for humanity? SARS-CoV-2 spike protein mutations. August 2020: An animation of coronavirus spike protein showing the SARS-CoV-2 spike protein fusion transformation. July 2020: An animation of coronavirus spike protein showing SARS-CoV-2 protein S priming by furin. March 2020: New Proteopedia page focused on the Coronavirus 2019 (COVID-19). January 2019: New morphing feature for Proteopedia, powered by PyMOL from from Schrodinger. January, 2018: 10th Anniversary Celebration Conference, University of Massachusetts, Amherst, USA. Group Photo of Participants. September, 2017: A workshop based on Proteopedia was held at the New Horizons in Biochemistry & Molecular Biology Education Conference, jointly organised by FEBS and IUBMB and hosted at the Weizmann Institute of Science. June, 2016: Animate any Proteopedia scene in Powerpoint. June, 2016: Proteopedia uses the Biological Assemblies from PDBe as the default scenes for all PDB entry pages. Thus, based on the curation by EBI (host for PDBe) the most biologically significant structure is shown. June, 2015: Award Ceremony for the the Proteopedia Award at the ICSG2015 - Deep Sequencing Meets Structural Biology, awarded on 10-Jun-2015 at the Weizmann Institute of Science December, 2014, Talking about Proteopedia on 12/04/14-12/06/14, a live online talk organised by DivCHED CCCE: Committee on Computers in Chemical Education October, 2014 Course in Spanish/English on Proteopedia and its uses to study, display and teach macromolecules. How to create fast loading pages in Proteopedia. How to be as safe as possible with Java Proteopedia on iPads! What version of Jmol is running? Proteopedia status Awards

Who knows ... Why is carbon monoxide so dangerous to breathe? How do Tamiflu & Relenza work as antiviral medication to and why do they sometimes fail? How do HIV drugs work to stop AIDS infection? How to design a human protein that can be expressed in bacteria? How does a repressor protein bind to a particular region of DNA? The Scoreboard Last 7 days (Top 10) Rank Score Pages Changes Username Score based on pages-edited and number-of-edits. List excludes members of the Proteopedia Team. All scores... Want To Contribute? Pages are easy to create and edit, and green links are fun & easy to make!  Step 1: Request an account (Members of the scientific community, including students and educators)  Step 2: Get started with the narrated video guide, then use the editing-help page as a reference  Step 3: Expand existing pages like HIV-1 protease, or start a new page on your favorite topic (We could use pages on RNA, adenylate kinase, & gamma-secretase, among others) Read The Articles eLIFE Labs 2016. The Journal of Structural Biology 2011. Genome Biology 2008 Contact Us