Structural Biologist / Professor / York University / servant of @miko_and_mika - photography - pottery - running / that's Thunder Bay above me
Toronto
Joined October 2008
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None of my designs were chosen for the @iGEM RBX-1 protein design competition. I had a lot of confidence in my #1 pick in @proteinbase --proteinbase.com/proteins/dar…. The very kind people at @adaptyvbio let me order an a la carte synthesis and I was pleased to learn that that candidate had 9 nM affinity.
The 107 aa candidate looked great during an orthogonal prediction challenge with AF3, Boltz2, Proteinix, an SeedFold with the stats to match (iLIS 0.79, ipSAE 0.84, actifpTM 0.97, ipTM 0.91) but on the ProteinBase site, the model suffered perhaps due to a lack of an MSA and the N-terminus of RBX-1 getting tangled up where it shouldn't be.
My overall strategy was to augment the beta sheet of RBX-1. I used @UWproteindesign Foundry (RFD3+MPNN+RF3) with a custom script that included Zn2+ and a selection block that rewarded maximum surface area and contacts.
I look forward to the next competition - it was a great learning experience to fill up my RTX-6000 linux box with the latest tools from the AI/Bio community. I have a structural biology lab at @YorkUniversity. Throughout my career, I have studied a variety of protein-protein and protein-nucleic acid interactions throughout my career.
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Here is a lightweight 1D/2D/3D NMR spectrum viewer for nmrPipe formated datasets. This is especially useful for Mac users who have missed nmrDraw for a long time. github.com/21tesla/NMRdraw_l… #NMR #NMRchat #BioNMR
Thank you to Frank Delagio (IBBR / U Maryland) for the original NMRdraw that has been used for decades and Johnthan Helmus (nmrglue.com) for the nmrglue framework that powers all the visualization and reads NMR data formats.
Hey @duolingo - can you replace, “There is a kitten in the trash can”? with a different practice sentence? Thank you.
ALT There is a kitten in the trash can
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@uOttawaNMR I have a 700 whose amplifier was away for over five months getting fixed. It's just arrived and I've noticed artifacts in spectra that come and go throughout the acquisition. Spectra affected use DIPSI-3 (CCH_TOCSY, for example). Any ideas?
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Making Up Proteins science.org/content/blog-pos…
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Logan Donaldson retweeted
Wonderful review by @RashikAhmed8 and Julie Forman-Kay about #NMR methods to study dynamic, multivalent complexes involving #IDPs/#IDRs
portlandpress.com/essaysbioc…
Logan Donaldson retweeted
Accurate Computational Design of 3D Protein Crystals by Li, Wang, Nattermann, ..., & Baker
Designing proteins that form crystals with specific lattice architectures such as space groups and tuned unit cell dimensions 🤯
doi.org/10.1101/2022.11.18.5…
Logan Donaldson retweeted
Possible self-awareness in penguins (preprint) biorxiv.org/content/10.1101/… I'm stealing Figure 2 as my indie album cover
Logan Donaldson retweeted
Meta just dropped 600+ million protein structure predictions, made using a large language model.
My latest for @Nature
nature.com/articles/d41586-0…
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Logan Donaldson retweeted
Our new approach for predicting protein 3D structure using single sequence + protein language model, w/o MSAs, is out. We combine a protein language model (AminoBERT) with a structural module using a transfer matrix formalism. (1/5)
Single-sequence protein structure prediction using a language model and deep learning go.nature.com/3fCqoAu
Logan Donaldson retweeted
NYT article about Maitland Jones, Jr.'s firing by the NYU administration | lots of interesting quotes from the NYU chemistry community nytimes.com/2022/10/03/us/ny…
