From emartz at microbio.umass.edu Tue Oct 5 18:24:34 2021 From: emartz at microbio.umass.edu (Eric Martz) Date: Tue, 5 Oct 2021 18:24:34 -0400 Subject: [Proteopedia] AlphaFold for students/young researchers, Oct 26 Message-ID: If you are a student or an early career researcher, you may wish to attend (electronically) this presentation: AlphaFold protein structure predictions - a step change for biology Sameer Velankar and Gerard Kleywegt, from the Protein Data Bank in Europe, and Alex Bateman, Head of Protein Sequence Resources, all at EMBL?s European Bioinformatics Institute (EMBL-EBI), explore the research avenues opened up by the AlphaFold database and explain the method's limitations. It is Tuesday October 26, 2021, at 19:00 CEST (13:00 US Eastern Time). Announcement with more info: https://network.febs.org/posts/alphafold-protein-structure-predictions-a-step-change-for-biology Advance registration is required: https://us02web.zoom.us/meeting/register/tZApduCurT0tGNLtFy1Vx4URQ3_kgxLlh2hX -Eric Martz for Fiona Viera McTiernan of the FEBS Network. From emartz at microbio.umass.edu Sat Oct 23 17:53:45 2021 From: emartz at microbio.umass.edu (Eric Martz) Date: Sat, 23 Oct 2021 17:53:45 -0400 Subject: [Proteopedia] Predict protein structure from sequence easily, free! Message-ID: <13833fa5-dc97-32ee-67a9-4c48cec55a4c@microbio.umass.edu> The AlphaFold project of DeepMind (Google) made a dramatic breakthrough in 2020. AlphaFold is often able to predict the structure of a protein from its sequence so well that the difference between the prediction and an X-ray crystallographic structure is as small as the difference between two independent X-ray determinations. Now, thanks to ColabFold, anyone can submit a sequence and get a free AlphaFold2 structure prediction. Its easy! Here are instructions: https://proteopedia.org/w/How_to_predict_structures_with_AlphaFold Reliability is estimated for each amino acid. FirstGlance in Jmol now automatically colors AlphaFold/ColabFold predictions by estimated reliability. Upload your predicted PDB file to http://bioinformatics.org/firstglance/fgij Snapshot of Alphafold2 Colab prediction displayed in FirstGlance colored by estimated reliability per residue: https://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Examples of AlphaFold2 Colab predictions ready to view instantly in FirstGlance: https://bioinformatics.org/firstglance/fgij/versions.htm * ColabFold - Making protein folding accessible to all by M. Mirdita, S. Ovchinnikov, & M. Steinegger: https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1 * More about AlphaFold: https://proteopedia.org/w/Alphafold * About the 2020 CASP blind competition: https://proteopedia.org/w/Theoretical_models * AlphaFold Database of several hundred thousand predictions: https://alphafold.ebi.ac.uk/ * Official Deepmind AlphaFold blog post: https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology -Eric Martz Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) University of Massachusetts, Amherst MA US Martz.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Sat Dec 4 13:28:01 2021 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Sat, 4 Dec 2021 18:28:01 +0000 Subject: [Proteopedia] 5,000 users Message-ID: <55F792A6-6B76-4188-ABB2-AC7ED5A68634@weizmann.ac.il> On December 4, 2021, the number of Proteopedia users went over 5,000!! The 5,000th user is from Juniata College, Huntingdon, Pennsylvania, US __ 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 emartz at microbio.umass.edu Sat Dec 4 14:21:49 2021 From: emartz at microbio.umass.edu (Eric Martz) Date: Sat, 4 Dec 2021 14:21:49 -0500 Subject: [Proteopedia] 5,000 users In-Reply-To: <55F792A6-6B76-4188-ABB2-AC7ED5A68634@weizmann.ac.il> References: <55F792A6-6B76-4188-ABB2-AC7ED5A68634@weizmann.ac.il> Message-ID: <675857ff-b5bc-5c93-9fc2-da0906574378@microbio.umass.edu> Congratulations Jaime! Your constant care and meticulous attention to creating, maintaining and improving Proteopedia is having ever wider impact! As I said over a decade ago, Proteopedia represents, in my opinion, a real, unique, and important breakthrough in structural biology communication. Congratulations also to Joel Sussman for his constant support via the Israel Structural Proteomics Center (ISPC) and his insights and encouragement, and to Eran Hodis who created the original Molecular Scene Authoring Tools. -Eric Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) University of Massachusetts, Amherst MA US Martz.MolviZ.Org On 12/4/21 1:28 PM, Jaime Prilusky wrote: > On December 4, 2021, the number of Proteopedia users went over 5,000!! > > The 5,000th user is from Juniata College, Huntingdon, Pennsylvania, US > > __ > Dr Jaime Prilusky > R&D Bioinformatics and Data Management > Life Sciences Core Facilities > Weizmann Institute of Sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Sat Dec 4 16:32:09 2021 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Sat, 4 Dec 2021 21:32:09 +0000 Subject: [Proteopedia] 5,000 users In-Reply-To: <675857ff-b5bc-5c93-9fc2-da0906574378@microbio.umass.edu> References: <55F792A6-6B76-4188-ABB2-AC7ED5A68634@weizmann.ac.il> <675857ff-b5bc-5c93-9fc2-da0906574378@microbio.umass.edu> Message-ID: <529F2117-B861-4174-BD31-3F438F734ABB@weizmann.ac.il> Thank you Eric, but you will agree that Proteopedia exists thanks to you and each and every one of the members of the Proteopedia User Community and Proteopedia contributors. Let's keep it that way! __ 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) On 4 Dec 2021, at 21:21, Eric Martz > wrote: Congratulations Jaime! Your constant care and meticulous attention to creating, maintaining and improving Proteopedia is having ever wider impact! As I said over a decade ago, Proteopedia represents, in my opinion, a real, unique, and important breakthrough in structural biology communication. Congratulations also to Joel Sussman for his constant support via the Israel Structural Proteomics Center (ISPC) and his insights and encouragement, and to Eran Hodis who created the original Molecular Scene Authoring Tools. -Eric Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) University of Massachusetts, Amherst MA US Martz.MolviZ.Org On 12/4/21 1:28 PM, Jaime Prilusky wrote: On December 4, 2021, the number of Proteopedia users went over 5,000!! The 5,000th user is from Juniata College, Huntingdon, Pennsylvania, US __ Dr Jaime Prilusky R&D Bioinformatics and Data Management Life Sciences Core Facilities Weizmann Institute of Sciences -------------- next part -------------- An HTML attachment was scrubbed... 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