Proteopedia:Hot News

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<div style='font-size:1.2em; padding:4px; font-weight:bold;'><!--[[Image:HTML5 Logo 512.png|32px]]--> Want faster, smoother rotation of large molecules?</div>
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As of Sunday, Jan 26 2014, Proteopedia displays interactive molecules in JSmol, without [[Java]]. Molecular scenes ("green links") can also be created and edited without Java. This enables Proteopedia to work on iPads, iOS and mobile devices where Java is not available, and on any device where Java is not installed. However, rotation is slower without Java, especially for large molecules (for example, the [[Ribosome]]).
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If your device has Java installed and working, you can achieve faster, smoother rotation by using Java: see
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[[Using_Java_for_Rendering_Structures|using Java for rendering structures]].
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<imagemap>
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Image:Animated_cavity.gif|frame|How to display cavities, pockets, and tunnels.
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default [[Jmol/Cavities_pockets_and_tunnels]]
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<div style='font-size:1.2em; padding:4px; font-weight:bold;'>What version of Jmol is running?</div>
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</imagemap>
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The version of Jmol currently running in Proteopedia is reported in the line ''JmolExtension'' at [[Special:Version]] in the column ''(now loaded Jmol version .....)''.
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* November 2024: [[How To Find A Structure]] is a new guide to finding an [[empirical models|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.
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* November 2024: [[How to predict structures with AlphaFold]] has been updated with instructions for the latest AlphaFold3 Server.
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<div style='font-size:1.2em; padding:4px; font-weight:bold;'>Proteopedia status</div>
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* November 2024: A handful of case studies illustrate what [[Nobel_Prizes_for_3D_Molecular_Structure#2020-2029|Nobel-Prize]] winning AlphaFold3 [[User:Eric_Martz/AlphaFold3_case_studies|can, and cannot, predict]].
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Proteopedia exceeded 2,500 registered users from 54 countries in November, 2013. In decreasing order, the 20 most represented countries are United States, Israel, Canada, France, United Kingdom, Germany, India, Italy, Japan, Australia, Austria, Denmark, Portugal, China, Finland, Chile, Brazil, Netherlands, Spain and Sweden.
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* November 2024: There is a new guide to being aware of, and dealing with [[missing residues and incomplete sidechains]].
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* March 2024: Professors are using Proteopedia for class projects in Brazil, Czech Republic, France, and various states in the USA. See the updated [[Proteopedia:News#Adoptions_in_College_and_University_Classes|Adoptions in College and University Classes]].
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Proteopedia currently contains over 3400 user-created articles, and over 93,000 automatically created pages corresponding to each of the structures released by the PDB.
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* What happens if a SARS-CoV-2 coronavirus enters your lung? See a clear explanation at [[Lifecycle of SARS-CoV-2]]
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* July 2022: <i class="fas fa-walking"></i> <i class="fas fa-running"></i> [[Exercise-induced N-lactoyl-phenylalanine, appetite and obesity]] <i class="fas fa-running"></i> <i class="fas fa-walking"></i>
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There are ~26,000 human visits and 59,000 bots visits weekly. The leading countries in accessing Proteopedia are the United States, Japan, Spain and China.
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* <i class="far fa-star bg-yellow"></i> <b>5,000 users!!</b> <i class="far fa-star bg-yellow"></i> On December 4, 2021, the number of Proteopedia users went over 5,000. The 5,000th user is from Juniata College, Huntingdon, Pennsylvania, US
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* ''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. [https://network.febs.org/posts/alphafold-protein-structure-predictions-a-step-change-for-biology Announcement]. [https://us02web.zoom.us/meeting/register/tZApduCurT0tGNLtFy1Vx4URQ3_kgxLlh2hX Registration].
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The most accessed pages, apart from the [[Main Page]], are [[Hemoglobin]], [[Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza]], [[Ribosome]], [[Acetylcholinesterase]], [[HIV-1_protease]], [[Green_Fluorescent_Protein]], [[Ramachandran_Plot]], [[1iyt]], [[Triose_Phosphate_Isomerase]], and [[Lac_repressor]]
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* A practical guide to teaching with Proteopedia <ref>doi 10.1002/bmb.21548</ref>
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* January 2021: How to display cavities, pockets, and tunnels? [[Jmol/Cavities_pockets_and_tunnels]]
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* December 2020: What is changing on SARS-CoV-2 virus and what this means for humanity? [[SARS-CoV-2 spike protein mutations]].
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<div style='font-size:1.2em; padding:4px; font-weight:bold;'>Awards</div>
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* August 2020: An animation of coronavirus spike protein showing the [[SARS-CoV-2 spike protein fusion transformation]].
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[[Poster_Prize_Awarded_at_7th-ICSG| Poster Prize Awarded at the 7th-ICSG]] Conference, Sapporo, Japan
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* July 2020: An animation of coronavirus spike protein showing [[SARS-CoV-2 protein S priming by furin]].
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* March 2020: New Proteopedia page [http://proteopedia.org/w/Coronavirus_Disease_2019_(COVID-19) focused on the Coronavirus 2019 (COVID-19)].
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* January 2019: New [http://proteopedia.org/cgi-bin/morph morphing] feature for Proteopedia, powered by PyMOL from from Schrodinger.
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* January, 2018: [[10th Anniversary Celebration Conference]], University of Massachusetts, Amherst, USA. [[Proteopedia:Scrapbook|Group Photo of Participants]].
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* September, 2017: A workshop based on Proteopedia was held at the [https://www.weizmann.ac.il/conferences/NHBMB2017 New Horizons in Biochemistry & Molecular Biology Education] Conference, jointly organised by FEBS and IUBMB and hosted at the Weizmann Institute of Science.
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* June, 2016: [[Help:Making animations for Powerpoint|Animate any Proteopedia scene in Powerpoint]].
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* June, 2016: Proteopedia uses the [[Biological_Unit|Biological Assemblies]] from [http://www.ebi.ac.uk/pdbe PDBe] as the default scenes for all PDB entry pages. Thus, based on the curation by [http://www.ebi.ac.uk EBI] (host for PDBe) the most biologically significant structure is shown.
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* June, 2015: [[Proteopedia:Scrapbook#Awards|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
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* December, 2014, [http://confchem.ccce.divched.org/2014FallCCCENLP9 Talking about Proteopedia] on 12/04/14-12/06/14, a live online talk organised by DivCHED CCCE: Committee on Computers in Chemical Education
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* October, 2014 [http://bit.ly/P14UAH Course] in Spanish/English on Proteopedia and its uses to study, display and teach macromolecules.
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* [[Create_fast_pages|How to create fast loading pages]] in Proteopedia.
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* [[Java#How_to_be_as_safe_as_possible_with_Java|How to be as safe as possible with Java]]
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* [[Main_Page_News#Proteopedia_on_iPads!|Proteopedia on iPads!]]
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* [[Main_Page_News#What_version_of_Jmol_is_running?|What version of Jmol is running?]]
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* [[Main_Page_News#Proteopedia_status|Proteopedia status]]
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* [[Main_Page_News#Awards|Awards]]
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<references/>

Current revision

How to display cavities, pockets, and tunnels.About this image
How to display cavities, pockets, and tunnels.
  1. ↑ Castro C, Johnson RJ, Kieffer B, Means JA, Taylor A, Telford J, Thompson LK, Sussman JL, Prilusky J, Theis K. A practical guide to teaching with Proteopedia. Biochem Mol Biol Educ. 2021 Jun 3. doi: 10.1002/bmb.21548. PMID:34080750 doi:http://dx.doi.org/10.1002/bmb.21548

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky, David Canner, Joel L. Sussman, Eran Hodis

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