@webflags1

Status and examples from https://xitter.cf/t.co/0V6todXpX6, an Atkinson lab tool. Is your pet protein encoded in a conserved neighbourhood? 🚩🚩🏴‍☠️🚩🚩 Tweets by @gem__atkinson

 Umeå University
webflags.se
Joined May 2020
  • Tweets204
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  • Followers181
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We are looking for a new PhD student to join us on our adventures in computational sequence and structural analyses of bacteriophage proteins atkinson-lab.com/phd-positio… You will be part of the new and exciting @scilifelab DDLS research school

PhD position available in high-throughput AlphaFold analyses of bacteriophage proteins

We are looking for a full-time bioinformatics PhD student to be involved in the DDLS project “Finding the prophages of Escherichia coli genomes and annotating the function of their genes usin…

atkinson-lab.com
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An interactive visualization of conserved gene neighborhoods now on corewiki.uni-goettingen.de/ (#SubtiWiki's next version)! It features clusters created with @webflags1 . Big thanks to Tom Nowak for his work and @gem__atkinson for the great FlaGs tool! @IMPRS_GS #bacillus #MOTY
Gene neighborhoods of rnpM across different organisms.

ALT Gene neighborhoods of rnpM across different organisms.

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WebFlaGs retweeted
LU-Fold@LU_Fold8 Nov 2023
Hello! LU-Fold now has an X presence! We are a Lund University facility for high throughput protein complex structure prediction. Follow for updates and click here for more info and request support atkinson-lab.com/lu-fold/

LU-Fold: a protein structure prediction facility at Lund University

Welcome to LU-Fold! LU-Fold is a Lund University-based facility for helping researchers predict protein structures of interest using the cutting-edge method AlphaFold2 (Nature Methods method of the…

atkinson-lab.com
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Here we go! A network of toxin-antitoxins, AlphaFold-modelling of thousands of complexes, experimentally validation, and discoveries about TA neutralisation and relationships to phage defence systems on the way biorxiv.org/content/10.1101/… @Lundsuni @medfak_LU @KAWstiftelsen

The structural basis of hyperpromiscuity in a core combinatorial network of Type II toxin-antitoxin...

Toxin-antitoxin (TA) systems are a large group of small genetic modules found in prokaryotes and their mobile genetic elements. Type II TAs are encoded as bicistronic (two-gene) operons that encode...

biorxiv.org
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Excited to announce that through @art_egorov's hard work we have a server version of uORF4u for uORF/leader peptide prediction server.atkinson-lab.com/uorf… Artyom has also made a home page for the Atkinson lab tools, including his MSA4u alignment visualiser server.atkinson-lab.com/
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Job alert! Structural bioinformatics research engineer position available in LU-Fold, a new facility in Lund University primarily for high-throughput prediction of protein:protein complexes with AlphaFold2. Please spread! lu.varbi.com/en/what:job/job…

Research engineer/engineer computational protein structure prediction

Description of the workplace We are looking to hire a Research engineer/Engineer who will establish a computational protein structure prediction facility in Lund University. The new facility, LU-Fold,

lu.varbi.com
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KAW-funded experimental PhD student position in mine and Gemma @gem__atkinson lab at Lund @medfak_LU to work toxin-antitoxins (and other exciting things!). #phage experience is a plus! please RT! lu.varbi.com/en/what:job/job…

PhD in Molecular biology

Background The focus of the Hauryliuk lab is molecular mechanisms of protein synthesis on the ribosome. We work on deciphering the molecular mechanisms implicated in bacterial virulence, tolerance to

lu.varbi.com
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Lovely to have been involved with this paper driven by Alex O'Neill and @MerianneMohamad, with beautiful structures from @naranson. Fun for @chayan and I to apply FlaGs @webflags1 to ABCFs and antibiotic resistance academic.oup.com/nar/advance…

Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target...

Abstract. The first member of the pleuromutilin (PLM) class suitable for systemic antibacterial chemotherapy in humans recently entered clinical use, under

academic.oup.com
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Playing with @webflags1 data today @gem__atkinson - I really didn't need any encouragement to go down the rabbit hole of MORE PROTEINS 😂
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Replying to @KieranBowran
@KieranBowran @chayan_saha7 @gem__atkinson @webflags1 get shout outs too
Microbiology Society@MicrobioSoc1 Apr 2021
In the latest #MicrobialMusings @GavinHThomas welcomes new Deputy EiC @proftracypalmer and highlights the latest papers published in #MicrobioJ doi.org/10.1099/mic.0.001053
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if you need a tool to look at gene neighbourhood conservation, I can recommend @webflags1 http://130.239.193.227/html/webFlaGs.html
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Cooperativity between the trigger factor and ClpXP: 'tig gene encoding the TF chaperone is frequently clustered with the clpPX - this prompted us to seek out the functional link between TF & ClpXP' Sounds like a target for @webflags1 ! nature.com/articles/s41467-0…
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The NCBI protein database is throwing some "bad gateway" errors today that is having a knock-on effect on webFlaGs. If your webFlaGs run using a single accession fails unexpectedly, please try again a little later, or use a sequence query instead
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