A freely available web platform for protein structure prediction and #cryoEM data analysis via #cloudcomputing at @SDSC_UCSD (Tweets mostly by @mcianfro)
San Diego, CA
Joined May 2016
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🚨Updates🚨 We have two updates to share: 1) We have updated #AlphaFold and #ColabFold to the latest version (v2.3.1) and 2) we added #ESMFold as a new structure prediction tool. Let us know how it goes for you! See thread ->
🚨Updated tool alert🚨 We have updated #modelangelo to v1.0.1. See thread below about changes - updates include working beautifully for protein, DNA, and RNA😍. Ex: PDB 8G1I / EMDB 29671 that has protein, dsDNA, and RNA xitter.cf/SjorsScheres/status/16…
1) Thew newly updated #AlphaFold2 and #ColabFold are faster and can predict up to 5500 amino acids (!!). NOTE: We merged all AlphaFold tools together so you'll find Multimer within the AlphaFold2 task
2) We added a new structure prediction tool: #ESMFold. #ESMFold utilizes protein sequence alone (no multiple sequence alignments) for structure prediction. It is ~5-10X faster than AlphaFold and offers a different approach for structure prediction. cosmic-cryoem.org/tools/esmf…
🚨New tool alert🚨 HHBlits - we added HHBlits searching to be used with #ModelAngelo building without sequence input running on our servers. Come give it a try!
🚨New tool alert🚨 Model Angelo - automated model building into #cryoEM maps using machine learning. Really nice results! Built the correct orientation and registry for a messy 3.8Å map from @cianfrocco_lab lab. cosmic-cryoem.org/2022/10/09…
🚨New tool alert🚨 Model Angelo - automated model building into #cryoEM maps using machine learning. Really nice results! Built the correct orientation and registry for a messy 3.8Å map from @cianfrocco_lab lab. cosmic-cryoem.org/2022/10/09…
Be sure to check out @SjorsScheres twitter thread on Model Angelo! xitter.cf/SjorsScheres/status/15…
🚨New tool alert🚨 Isonet refine. We are excited to include the first #teamtomo tool for #cryoET onto COSMIC2! Isonet is a generative deep learning tool that attempts to remove the missing wedge from tomograms. Hopefully, more #cryoET tools to come! cosmic-cryoem.org/tools/ison…
COSMIC CryoEM retweeted
Here, I'll talk about how we use @globus for data transfer into @CosmicCryoEM and using @globus for moving data in/out of @awscloud for our @UMLifeSciences #cryoEM workshop
Data management is becoming increasingly complex. Join us for expert tips on how to address these challenges & hear from @mcianfro on how @globus—together with AWS—helps him manage the massive amounts of research data generated by microscopes. go.aws/3D4de9k
What protein structure prediction software should you use on #COSMIC2? Here is a brief primer comparing the five different prediction tools:
cosmic-cryoem.org/2022/08/30…
🚨New tool alert🚨 #OmegaFold is now available on #COSMIC2. #OmegaFold does not require multiple sequence alignments making it well-suited for low sequence coverage proteins. It can also run on sequences up to 4096 AA. Try it out! cosmic-cryoem.org/tools/omeg…
🚨New tool alert🚨 IgFold - A tool to predict accurate antibody structures that is faster (and sometimes more accurate) than #AlphaFold [@jeffreyjgray lab] cosmic-cryoem.org/tools/igfo…
Ever wanted to upload a #cryoSPARC particle stack into COSMIC2? We put together documentation describing how you can go from cryoSPARC extracted stacks to COSMIC2 🎉 Now you can go straight from cryoSPARC to #RELION or #cryoDRGN cosmic-cryoem.org/2022/06/21…
COSMIC CryoEM retweeted
👇 An old script from grad school that uses SPIDER to align averages with a 3D volume. A tried and true script that confirms my 3D maps match class averages. Essential for my PhD work mapping conformational changes in TFIID pubmed.ncbi.nlm.nih.gov/2333…
🚨New tool alert🚨 Ever wanted to compare a 3D reconstruction or a PDB with #cryoEM 2D class averages? We added a tool that will find the best matching projections of an MRC or PDB with 2D averages. cosmic-cryoem.org/tools/alig…
🚨New tool alert🚨 Ever wanted to compare a 3D reconstruction or a PDB with #cryoEM 2D class averages? We added a tool that will find the best matching projections of an MRC or PDB with 2D averages. cosmic-cryoem.org/tools/alig…
This is a great way to check if an #AlphaFold prediction matches your 2D averages. OR confirming that your 2D averages match your ab initio or 3D refined maps 💅
COSMIC CryoEM retweeted
Early registration deadline for @ACAxtal #aca2022 is May 31st.
Want to receive hands-on training with #cryoEM sample preparation instrumentation? Sign up for WK-5: CryoEM sample preparation training held at @CryoEM_PNCC during workshop Friday 7/29/2022.
amcac.memberclicks.net/aca-w… – at Portland, OR
Early registration for #acameeting2022 #acamtg2022 #aca2022meeting #Portland ends in one week! Register today to save! #crystallography #structuralscience #cryoem #sciencetwitter #chemistry #diffraction #Biology #xrd #bio acameeting.com
🚨New tool alert🚨 #ColabFold is now available on #COSMIC2. It is faster and offers slightly different results and options than #AlphaFold, cosmic-cryoem.org/tools/cola…
COSMIC CryoEM retweeted
We are looking for a Senior Scientific Software Engineer to develop new software tools for modeling large molecular complexes. Perfect balance between academic research and software development. #python #programming, #AlphaFold, #cryoEM. Apply here:
embl.org/jobs/position/HH002…
