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Jinwoo Leem Profile picture
Jinwoo Leem
@ideasbyjin
Director of ML @alchemabtx prev: @benevolent_ai, @OPIGlets. Antibodies, LLMs, protein structure prediction, neuro, onco. 🇨🇦🇬🇧🇰🇷 Tweets=my views.
Nov 23, 2022 • 5 tweets • 3 min read
Ran some experiments! #ImmuneBuilder is better than #ESMFold (@alexrives / @TomSercu), right? There are advantages of using the latter, and now a 🧵 on why getting carried away with low RMSDs is only a part of the story...(1/5)
#machinelearning #proteins First, the metrics are RMSDs based on aligning the C/N/CA/CB atoms across the chain, then calculating the RMSD across a region. i.e. align every residue of the VH, then calculate RMSD across CDRH3, or CDRH1, etc. This is on ~35 antibodies of the ImmuneBuilder test set (2/5)
Nov 19, 2022 • 7 tweets • 3 min read
Pretty wild that there have been at least 4-5 antibody-specific structure prediction tools this year, all based on #deeplearning

1. DeepAb/IgFold (@jeffruffolo)
2. ABLooper/ImmuneBuilder (@brennanaba)
3. Equifold (@jaehyeon_lee_ml)
4. t-AbFold

What does this mean? 🧵(1/6) First, it's pretty crazy we even have antibody-specific tools, since #AlphaFold2, #ESMFold, #OmegaFold, all do a decent job at antibody modelling. However, antibody-specific tools have -some- feature that's necessary (e.g. being MSA-free) (2/6)
Jun 6, 2022 • 5 tweets • 3 min read
Exciting work from @KathyYWei1, @AmeyaHarmalkar & @proteinrosh on predicting scFv developability. TLDR: transformers and CNNs can potentially help prioritise mutations sites for enhancing stability (1/5) #antibodies #machinelearning #proteineng Context: a single-chain Fv (scFv) is an antibody construct whose heavy and light chains are linked. It's not the conventional "Y" shape molecule, and is useful for engineering / phage display, etc. See @AlissaHummer's post blopig.com/blog/2021/07/a… (2/5)
May 26, 2022 • 6 tweets • 3 min read
A "negative" result, but phenomenal thought piece from @naturalantibody / @antibodymap. TLDR predicting antibody-antigen interactions is pretty darn hard (1/5) #antibodies #machinelearning #alphafold

naturalantibody.com/use-case/deepm… Predicting Ab-Ag interactions is a sub-problem of the protein-protein interaction problem. There are many facets to consider here, including but not limited to, identifying the correct antigen (let alone the correct epitope), the correct paratope, orientation, etc (2/5)
May 19, 2022 • 7 tweets • 6 min read
Really excited to announce that AntiBERTa is now published in @Patterns_CP! Here we describe a transformer model that demonstrates understanding of antibody sequences 🧵 (1/6)

#machinelearning #antibodies #drugdiscovery
cell.com/patterns/fullt… We pre-train a transformer model based on RoBERTa. We exclusively use full-length antibody/B-cell receptor sequences using the MLM objective. Other similar transformers FYI include BioPhi (@prihodad), ABLang (@HegelundOlsen), AntiBERTy (@jeffruffolo) (2/6)