ML for Protein Engineering Seminar
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ml4proteins.bsky.social
ML for Protein Engineering Seminar
@ml4proteins.bsky.social
240 followers 2 following 11 posts
Seminar series on machine learning for protein engineering. Details for seminars and slack are on our website. DM us if you're interested in presenting! ml4proteinengineering.com
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ml4proteins.bsky.social
Next Tues (6/3) at 4PM ET, we will have @avapamini.bsky.social
present "Deep learning guided design of protease substrates"

Paper: www.biorxiv.org/content/10.1...

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Deep learning guided design of protease substrates
Proteases, a class of enzymes that play critical roles in health and disease, exert their function through the cleavage of peptide bonds. Identifying substrates that are efficiently and selectively cl...
www.biorxiv.org
May 27, 2025 at 9:10 PM
ml4proteins.bsky.social
Next Tues (5/20) at **2PM ET**, we will have Woody Ahern and Jason Yim present "Atom level enzyme active site scaffolding using RFdiffusion2"

Paper: www.biorxiv.org/content/10.1...

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Atom level enzyme active site scaffolding using RFdiffusion2
De novo enzyme design starts from ideal active site descriptions consisting of constellations of catalytic residue functional groups around reaction transition state(s), and seeks to generate protein ...
www.biorxiv.org
May 14, 2025 at 9:59 PM
ml4proteins.bsky.social
Next Tues (5/13) at 4PM ET, we will have Anna Lauko and Sam Pellock present "Computational design of serine hydrolases"

Paper: www.science.org/doi/10.1126/...

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Computational design of serine hydrolases
The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of ...
www.science.org
May 9, 2025 at 2:01 AM
ml4proteins.bsky.social
Next Tues (4/29) at **4:30PM** ET, we will have @ginaelnesr.bsky.social @hkws.bsky.social present "Learning millisecond protein dynamics from what is missing in NMR spectra"

Paper: biorxiv.org/content/10.1...

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Learning millisecond protein dynamics from what is missing in NMR spectra
Many proteins’ biological functions rely on interconversions between multiple conformations occurring at micro-to millisecond (µs-ms) timescales. A lack of standardized, large-scale experimental data ...
biorxiv.org
April 22, 2025 at 9:08 PM
ml4proteins.bsky.social
Next Tues (4/1) at **11AM** ET we will have Anthony Marchand present "Targeting protein–ligand neosurfaces with a generalizable deep learning tool"

Paper: www.nature.com/articles/s41...

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Targeting protein–ligand neosurfaces with a generalizable deep learning tool - Nature
A computational deep learning approach is used to design synthetic proteins that target the neosurfaces formed by protein–ligand interactions, with applications in the development of new therapeutic m...
www.nature.com
March 26, 2025 at 5:24 PM
ml4proteins.bsky.social
Next Tues (3/18) at 4PM ET we will have Alan Amin
present "Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences"

Paper: arxiv.org/abs/2412.07763

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Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences
To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from larg...
arxiv.org
March 11, 2025 at 9:08 PM
ml4proteins.bsky.social
Next Tues (3/4) at 4PM ET we will have Karsten Kreis present "Proteina: Scaling Flow-based Protein Structure Generative Models"

Paper: openreview.net/forum?id=TVQ...

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Proteina: Scaling Flow-based Protein Structure Generative Models
Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale flow-based...
openreview.net
February 25, 2025 at 10:05 PM
ml4proteins.bsky.social
Next Tues (2/18) at **5PM ET** we will have @hannes-stark.bsky.social and Bowen Jing present "ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids"

Paper: openreview.net/forum?id=0ct...

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ProtComposer: Compositional Protein Structure Generation with 3D...
We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference...
openreview.net
February 13, 2025 at 6:51 PM
ml4proteins.bsky.social
Next Tuesday, 2/4 @ 4 pm EST, Aya Ismail and Nathan Frey will present "Concept Bottleneck Language Models"
Paper: arxiv.org/abs/2411.06090
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Concept Bottleneck Language Models For protein design
We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept. Our architecture offers thr...
arxiv.org
January 29, 2025 at 9:15 PM
ml4proteins.bsky.social
Next Tuesday, 1/21 @ 4 pm EST, Elana Simon
will present "InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders"

Paper: www.biorxiv.org/content/10.1...

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InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
Protein language models (PLMs) have demonstrated remarkable success in protein modeling and design, yet their internal mechanisms for predicting structure and function remain poorly understood. Here w...
www.biorxiv.org
January 14, 2025 at 10:05 PM
ml4proteins.bsky.social
This Tuesday, 1/7 @ 4 pm EST, we'll be back with the 2025 seminar series!

Seyone Chithrananda will present "Mapping the combinatorial coding between olfactory receptors and perception with deep learning"

Paper: biorxiv.org/content/10.1...

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Mapping the combinatorial coding between olfactory receptors and perception with deep learning
The sense of smell remains poorly understood, especially in contrast to visual and auditory coding. At the core of our sense of smell is the olfactory information flow, in which odorant molecules acti...
biorxiv.org
January 6, 2025 at 12:57 AM