From emartz at microbio.umass.edu Sun Jul 5 18:55:50 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Sun, 5 Jul 2020 18:55:50 -0400 Subject: [Proteopedia] Proteopedia recent problems believed to be fixed In-Reply-To: <1442cb99-e97a-60f7-e9a0-044fd229a40b@microbio.umass.edu> References: <12938041-7CB0-4148-8C93-5F1CE1DC5864@weizmann.ac.il> <00ca01d6529e$6896c4f0$39c44ed0$@midlink.co.il> <1442cb99-e97a-60f7-e9a0-044fd229a40b@microbio.umass.edu> Message-ID: <6bc8164d-433c-d198-8658-88268637390b@microbio.umass.edu> Dear Proteopedia Users: Several weeks ago, some changes were made by AWS affecting the servers that provide Proteopedia.Org. Inadvertently, these caused some problems, which included: - Sometimes a delay of about 20 sec before a Proteopedia page displayed in the browser. - After saving edits to a page, the edits did not show until after a substantial delay. - Clicking "Random" (in the "navigation" box at the upper left) displayed the same page over and over, instead of a new random page on each click. Thanks to Jaime Prilusky, we believe these problems have been fixed. Please always report any suspected problems you may observe to contact at proteopedia.org. Thank you! -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) University of Massachusetts, Amherst MA US Martz.MolviZ.Org Proteopedia.Org Administrator User:Eric_Martz -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Mon Jul 27 18:08:03 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Mon, 27 Jul 2020 18:08:03 -0400 Subject: [Proteopedia] Animation of Coronavirus Spike Protein Priming Message-ID: I have just completed a new article that animates the conformational change induced in the coronavirus spike protein by proteases such as furin. This change facilitates the initial step of virus binding to the host cell's ACE2 receptor. http://proteopedia.org/wiki/index.php/SARS-CoV-2_protein_S_priming_by_furin Suggestions are, of course, most welcome (or you can edit the page yourself). -Eric Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) U Mass, Amherst -- Martz.MolviZ.Org * Guided Exploration of Macromolecules: FirstGlance.Jmol.Org * Protein 3D Structure Wiki: Proteopedia.Org * Top Five 3D MolVis Tools: Top5.MolviZ.Org * Education: Biochem in 3D at MolviZ.Org * Find Functional Patches in Proteins: ConSurf * Atlas of Macromolecules: Atlas.MolviZ.Org * Interactive Molecules in Architectural Spaces: MolecularPlayground.Org * Workshops: Workshops.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Mon Aug 17 15:27:56 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Mon, 17 Aug 2020 15:27:56 -0400 Subject: [Proteopedia] Coronavirus spike protein priming and fusion Message-ID: <85002af9-9bbb-1f58-74c1-0752382ca52b@microbio.umass.edu> I have completed 2 new tutorials: http://proteopedia.org/w/SARS-CoV-2_spike_protein_priming_by_furin http://proteopedia.org/w/SARS-CoV-2_spike_protein_fusion_transformation Each includes interactive morph animations, and downloadable Powerpoint-ready animations. These are based on recent cryo-EM structures of multiple conformations. A protease (typically furin, ample in the lungs) clips spike protein, inducing the extension of a receptor-binding surface to engage the ACE2 receptor on the host cell. The mechanism of membrane fusion, which deposits the viral RNA inside the host cell initiating infection, appears similar to that of influenza hemagglutinin. The spike protein "spears" the host cell membrane, capturing it with a "fusion peptide", and pulls the virus membrane very close. Fusion has been seen in molecular dynamics simulations (see Figure 2 in the fusion link). Spike protein has a cavity that is the target of drug screening (see Figure 4 in the fusion link). A cute graphical abstract shows a 3-legged folding stool as an analogy to spike protein, with the drug-target cavity between its legs (see Figure 3 in the fusion link). For those developing educational tutorials, consider listing them at http://Merlot.Org, a well- and long-established catalog of educational resources. See for example what I've listed there: https://www.merlot.org/merlot/materials.htm?userId=14545&fromAdvancedSearch=true&sort.property=dateCreated -Eric Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) U Mass, Amherst -- Martz.MolviZ.Org * Guided Exploration of Macromolecules: FirstGlance.Jmol.Org * Protein 3D Structure Wiki: Proteopedia.Org * Top Five 3D MolVis Tools: Top5.MolviZ.Org * Education: Biochem in 3D at MolviZ.Org * Find Functional Patches in Proteins: ConSurf * Atlas of Macromolecules: Atlas.MolviZ.Org * Interactive Molecules in Architectural Spaces: MolecularPlayground.Org * Workshops: Workshops.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Tue Sep 29 02:10:35 2020 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Tue, 29 Sep 2020 06:10:35 +0000 Subject: [Proteopedia] JSmol version on SAT Message-ID: <95D15DDA-159A-4E56-9FA7-46D67BC880D1@weizmann.ac.il> Dear Proteopedia Users: Both SAT (Scene Authoring Tool) and Proteopedia pages now follow the Misc Preferences and will use a JSmol version based on the '[ ] Use latest version of JSmol ...' selection. Until now, all Proteopedia pages (except SAT) rendered models using either the default JSmol on Proteopedia or the latest version @ https://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js depending on the setting of the appropriated User Preference. This allows to fully test new versions of JSmol before adopting them as default for Proteopedia. Regards, Jaim __ Dr Jaime Prilusky R&D Bioinformatics and Data Management Life Sciences Core Facilities Weizmann Institute of Sciences jaime.prilusky at weizmann.ac.il Phone: 972-8934-4959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -------------- next part -------------- An HTML attachment was scrubbed... URL: From joel.sussman at weizmann.ac.il Tue Sep 29 02:28:57 2020 From: joel.sussman at weizmann.ac.il (Joel Sussman) Date: Tue, 29 Sep 2020 06:28:57 +0000 Subject: [Proteopedia] JSmol version on SAT In-Reply-To: <95D15DDA-159A-4E56-9FA7-46D67BC880D1@weizmann.ac.il> References: <95D15DDA-159A-4E56-9FA7-46D67BC880D1@weizmann.ac.il> Message-ID: <9796AF37-1008-4DC9-9E11-877E74127E8D@weizmann.ac.il> Dear Jaime This sounds very very good Thanks Yoel Sent from my iPhone > On Sep 29, 2020, at 09:10, Jaime Prilusky wrote: > > ?Dear Proteopedia Users: > > Both SAT (Scene Authoring Tool) and Proteopedia pages now follow the Misc Preferences and will use a JSmol version based on the '[ ] Use latest version of JSmol ...' selection. > > Until now, all Proteopedia pages (except SAT) rendered models using either the default JSmol on Proteopedia or the latest version @ https://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js depending on the setting of the appropriated User Preference. > > This allows to fully test new versions of JSmol before adopting them as default for Proteopedia. > > Regards, > Jaim > __ > Dr Jaime Prilusky > R&D Bioinformatics and Data Management > Life Sciences Core Facilities > Weizmann Institute of Sciences > > jaime.prilusky at weizmann.ac.il > Phone: 972-8934-4959 > > OCA, http://oca.weizmann.ac.il (the protein structure/function database) > Proteopedia, http://proteopedia.org (because life has more than 2D) > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > _______________________________________________ > Proteopedialist-for-users mailing list > Proteopedialist-for-users at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users From jaime.prilusky at weizmann.ac.il Wed Sep 30 10:36:34 2020 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Wed, 30 Sep 2020 14:36:34 +0000 Subject: [Proteopedia] New JSmol version 14.31.8 Message-ID: <5CABE4E6-284A-4049-965F-3A88C5648B4C@weizmann.ac.il> Dear Proteopedia Users, Proteopedia runs now on the latest version of JSmol: 14.31.8 Please clear your browser's cache if something stops running. Jaim