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Roland Dunbrack 🏳️‍🌈 Profile picture
Roland Dunbrack 🏳️‍🌈
@RolandDunbrack
Computational structural biologist at the Fox Chase Cancer Center. Out and proud. Pronouns: he, his, him. I'm the shorter one. Living with CLL/SLL.
Oct 17, 2022 • 16 tweets • 7 min read
In the works for a LONG while - a new clustering of antibody CDR structures to update North et al (2011)/PyIgClassify. Clusters now have high electron density support & at least 10 sequences. DBSCAN helped to remove noise points. @biorxiv_bioinfo @build_models @PDBeurope @PDBj_en The website has been updated w/ the new data. dunbrack2.fccc.edu/PyIgClassify2. Downloads include mmCIF coordinates, data per domain & per cdr, & fasta sequences. Paper is work by Simon Kelow, Bulat Faezov (@Bulat41292666), website by @QifangXu. Advice from Jared Adolf-Bryfogle @jadolfbr.
Oct 15, 2022 • 7 tweets • 1 min read
Waiting for a biorxiv paper to post is like watching water boil. I know they're busy....
Aug 22, 2022 • 15 tweets • 8 min read
Examples from our Protein Common Assembly Db now on @biorxiv_bioinfo with @QifangXu. Viable assemblies for all Xray structures (EPPIC, @josemduarte), clustered w/ cryoEM, NMR assemblies by Pfam architectures + stoichiometry+ symmetry + interfaces. @buildmodels @PDBeurope @pdbj_en We count "Crystal forms (CFs)" - unique crystal unit cells or cryo-EM or NMR experiments for each cluster, and number of uniprot sequences across each cluster. More experimental data --> more support for relevance of biological assembly. Also #PDB's bioassemblies, PISA, EPPIC.
Jun 22, 2020 • 10 tweets • 6 min read
I can't figure out what the hell this image is supposed to be. That's not what RNA or DNA look like. Scientific American (@sciam) should promote scientific visual literacy not pseudoscientific stock photos. @WrongHandedDNA will love this. Image @WrongHandedDNA is one of my favorite twitter accounts. I post to it when I am in this kind of mood: Image
Mar 8, 2020 • 14 tweets • 6 min read
@deray OK, give me a few minutes to write a thread. But I'll start with - it's like the difference between squirrels and raccoons." Quite different species. Different branches of vertebrates. Ultimately related (like humans and mice) but distantly. @deray First, viruses are particles that are much smaller than cells (like human skin cells, nerve cells). They have some kind of shell (of proteins or lipids - fat-like molecules) and inside they have a chromosome (like our 46) - information to build new copies of the virus.