SLiM propagandists Migrating to @slim-team.bsky.social
London, England
Joined June 2014
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Excited to present a new docking motif for IKK (Inhibitor of κB (IκB) kinase)! A great collaboration with the Zanier lab at the ESBS showed a YDDΦxΦ motif in IκBα, IκBβ and p100 recruits IKK.
nature.com/articles/s41467-0…
There's an associated database to make it easier to explore the data. Check it out here slim.icr.ac.uk/cell_cycle/
Congratulations to @hazemsci on his new paper "xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures" in Biomolecules. The tool maps evolutionary info onto #alphafold/pdb structures to find putative functional surfaces. mdpi.com/2318554.
The latest steps in our long running collaboration with the @Ivarssonlab! Human short linear motif discovery is now high-throughput - we characterise 40 motif-binding domains by screening them against a library of ~ 1,000,000 overlapping peptides in a single binding assay.
@_BalintMeszaros and I have been staring at the @DeepMind @emblebi structure database non-stop. To see them in context we've updated ProViz to visualise AlphaFold2 data mapped to multiple sequence alignments and data from @uniprot @rcsbPDB @PfamDB tinyurl.com/ProVizAF.
ALT Example of ProViz - Alphafold on MDM2 showing AlphaFold2 data (per residue AlphaFold2 pLDDT scores, normalised surface accessibility scores, neighbourhood crowding, secondary structure). The data is mapped to multiple sequence alignments, structure data from @PDBeurope, domain data from @PfamDB, feature data from @uniprot and IDR data from MobiDb.
For anyone interested in sequence gazing at the SARS CoV 2 proteins and their homologues we've uploaded the alignments ito the ProViz visualisation tool (slim.icr.ac.uk/proviz/). Hopefully someone will see something useful.
