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Possu Huang Lab

@possuhuanglab.bsky.social
512 followers 39 following 31 posts

Our lab uses experimental and computational methods to design de novo proteins | @Stanford

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Reposted by Possu Huang Lab
Pauline Funchain @funchainmd.bsky.social · 04/11/2025
Ever wonder why our HLA specified cancer therapies are only for HLA02:01 thus far? @possuhuanglab.bsky.social presents the scope of the problem at the inaugural @stanford-cancer.bsky.social AI and Cancer Research Symposium 🧬
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
Read our preprint here: www.biorxiv.org/content/10.1... (8/8)
biorxiv.org
SLAE: Strictly Local All-atom Environment for Protein Representation
Building physically grounded protein representations is central to computational biology, yet most existing approaches rely on sequence-pretrained language models or backbone-only graphs that overlook...
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
Work done by Yilin Chen, @tianyu.bsky.social , Cizhang Zhao and @hkws.bsky.social . Thank you all! (7/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
SLAE projects all-atom structures onto a smooth manifold! Unguided linear interpolation between conformations in SLAE latent space decodes to coherent intermediates structures. (6/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
SLAE extends our generative coverage assessment SHAPES to all-atom, per-residue-type granularity. Now we can compare de novo all-atom protein design models and spot residue-level environment biases. (5/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
Rich in atomic-environment signal, SLAE features outperform PLMs and task-specific models across diverse, challenging downstream tasks, including binding affinity, thermostability and chemical shift prediction. All-atom structure pretraining is all you need! (4/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
The SLAE latent landscape is organized in meaningful ways beyond amino acid identity. It separates residue embeddings along features including solvent accessibility, secondary structure and structural nativeness. (3/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
We design a deliberately hard two-part task to learn compact, expressive features: a local graph encoder projects each residue’s atomic interactions into a feature vector, while a global decoder learns to compose these local environment tokens into coherent macromolecules. (2/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 09/10/2025
Introducing SLAE, our new framework to represent all-atom protein structures with residue local chemical environment tokens! SLAE reasons over atomic interactions to recover structures and residue pairwise energetics, yielding a generalizable, physics-informed latent space. (1/8)
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Possu Huang Lab @possuhuanglab.bsky.social · 26/08/2025
💻 Sampling and training code for Protpardelle-1c is now available: github.com/ProteinDesig... Feedback and requests are welcome!
github.com
GitHub - ProteinDesignLab/protpardelle-1c: Updated Protpardelle models with more robust motif scaffolding and multichain support
Updated Protpardelle models with more robust motif scaffolding and multichain support - ProteinDesignLab/protpardelle-1c
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Possu Huang Lab @possuhuanglab.bsky.social · 19/08/2025
Code will be released soon on our GitHub: github.com/ProteinDesig... Preprint: www.biorxiv.org/content/10.1... Have fun sampling and training!
biorxiv.org
Conditional Protein Structure Generation with Protpardelle-1c
We present Protpardelle-1c, a collection of protein structure generative models with robust motif scaffolding and support for multi-chain complex generation under hotspot-conditioning. Enabling sidech...
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Possu Huang Lab @possuhuanglab.bsky.social · 19/08/2025
Our new set of all-atom models can sample plausible sidechains without stage-2 sampling. Sequence-dependent partial diffusion behavior occurs when we mask the dummy atoms.
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Possu Huang Lab @possuhuanglab.bsky.social · 19/08/2025
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Possu Huang Lab @possuhuanglab.bsky.social · 19/08/2025
We achieve competitive results on MotifBench and the RFdiffusion/La-Proteina motif scaffolding benchmarks with both backbone-only and all-atom models, proposing scaffolds to previously unsolved problems.
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Possu Huang Lab @possuhuanglab.bsky.social · 19/08/2025
We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation.
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Possu Huang Lab @possuhuanglab.bsky.social · 29/07/2025
Paper: authors.elsevier.com/a/1lWEe8YyDf...
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Possu Huang Lab @possuhuanglab.bsky.social · 29/07/2025
We include some additional analysis in the supplement, including secondary structure distributions.
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Possu Huang Lab @possuhuanglab.bsky.social · 29/07/2025
SHAPES now published in Cell Systems!
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Reposted by Possu Huang Lab
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 21/02/2025
All-atom fixed backbone protein sequence design with FAMPNN @richardshuai.bsky.social Talal Widatalla @possuhuanglab.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...
FAMPNN architecture
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Reposted by Possu Huang Lab
Mohammed AlQuraishi @moalquraishi.bsky.social · 15/01/2025
I'm organizing a Keystone symposium, along with Liz Kellogg and @possuhuanglab.bsky.social, on machine learning and macromolecules. Mar 23-26 in Keystone, Colorado. We have a great lineup and deadlines are coming up soon!
keystonesymposia.org
Machine Learning Applied to Macromolecular Structure and Function | Keystone Symposia
Join us at the Keystone Symposia on Machine Learning Applied to Macromolecular Structure and Function, March 2025, in Keystone, with field leaders!
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Reposted by Possu Huang Lab
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 15/01/2025
A framework for evaluating how well generative models of protein structure match the distribution of natural structures. @possuhuanglab.bsky.social www.biorxiv.org/content/10.1...
Generative models capture a biased set of protein structure spaceGenerative models do not capture the full expressivity of PDB structuresProtein structure embeddings reveal undersampled and de novo structure space
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Possu Huang Lab @possuhuanglab.bsky.social · 15/01/2025
Preprint: www.biorxiv.org/content/10.1... Code: github.com/ProteinDesig... Dataset: zenodo.org/records/1458...
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Possu Huang Lab @possuhuanglab.bsky.social · 15/01/2025
Our supplement has many additional figures of the rasterized protein structure space, stratified by designable and not designable and spatially organized by ESM3 and ProtDomainSegmentor embeddings.
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Possu Huang Lab @possuhuanglab.bsky.social · 15/01/2025
One consequence of unbiased sampling of protein structure space is a higher likelihood of finding TERtiary Motifs (TERMs) which involve complex loops, with implications for functional protein design (see Figure 5 legend for group labels).
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Possu Huang Lab @possuhuanglab.bsky.social · 15/01/2025
Inspired by the FPD metric in EvoDiff for protein sequence distributions, we compute Fréchet distance using protein structure embeddings, also subsetted to designable and non-designable samples (FPD-D and FPD-ND).
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Possu Huang Lab @possuhuanglab.bsky.social · 15/01/2025
New preprint from our group! We propose SHAPES, a set of metrics to quantify the distributional coverage of generative models of protein structures with embeddings at different structural hierarchies and quantify undersampling / extrapolation behaviors.
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Reposted by Possu Huang Lab
Daniel Hoces @dhoces.bsky.social · 17/12/2024
This is a clever way to use synthetic biology: taking a toxin that overactivate the immune system (superantigen), rationally modify its core components and transform it into a platform of immunotherapy agents. Congratulations to @haotiandu.bsky.social and @possuhuanglab.bsky.social on the 2 papers!
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Reposted by Possu Huang Lab
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 17/12/2024
Checkout out these two bombshell papers from @possuhuanglab.bsky.social @stanfordmedicine.bsky.social, computational design of antigen-specific binders to MHC-I or -II, with applications to next gen targeted therapeutics 🤯
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Reposted by Possu Huang Lab
Stanford Department of Bioengineering @bioe-stanford.bsky.social · 17/12/2024
Science in 60 Seconds: Haotian Du, PhD student with Possu Huang’s lab, explains her research on creating novel proteins that expands the possibilities for detecting more cancer types. @possuhuanglab.bsky.social @haotiandu.bsky.social
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Reposted by Possu Huang Lab
Stanford Department of Bioengineering @bioe-stanford.bsky.social · 17/12/2024
Incredible work from BioE Professor’s Possu Huang Lab @possuhuanglab.bsky.social @haotiandu.bsky.social - pioneering novel proteins with new structures and functions, unlocking new possibilities for detecting more cancer types. Congratulations!
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
@haotiandu.bsky.social is now on BlueSky 😄
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Reposted by Possu Huang Lab
haotiandu.bsky.social @haotiandu.bsky.social · 17/12/2024
Excited to share that TRACeR stories are out🙌
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Reposted by Possu Huang Lab
Jon Douglas @atranscendedman.bsky.social · 15/12/2024
A new system, TRACeR-I, targets peptides on MHC I molecules with high precision, enabling specific tumor and virus cell killing. It powers CAR-T and BiTE therapies, showing potential to transform cancer and infectious disease treatment. www.nature.com/articles/s41...
nature.com
Targeting peptide antigens using a multiallelic MHC I-binding system - Nature Biotechnology
A protein platform rapidly develops peptide-focused major histocompatibility complex class I binders with high specificity.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
The TRACeR project was led by Haotian Du and Jingjia Liu and a collaborative effort between the Huang Lab at @bioe-stanford.bsky.social, Stanford BioX and the Sgourakis Lab at UPenn/CHOP @naturebiotech.bsky.social @stanfordmedicine.bsky.social @uofpenn.bsky.social @stanfordbiosci.bsky.social
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
7/ Our platform offers a convenient strategy for creating MHC binders: from a master library, peptide-specific MHC binders can be isolated simply by a few rounds of yeast surface display enrichment.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
6/ We show proof-of-concept targeted killing of tumor cells using TRACeR-I.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
5/ The mechanism of TRACeR-1 can achieve discrimination of single point mutants to peptides.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
4/ But MHC-I peptides have bulged conformations. For TRACeR-I, we use a set of spatially-defined amino acid residues to “box-in” on the peptide and achieve recognition.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
3/ Peptides in MHC-II are in an extended conformation. TRACeR-II uses a surface loop to reach into MHC-II’s peptide binding groove to recognize the peptide. We use a single loop to convey specificity to the peptide in the binding groove.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
2/ MHC antigens are central to the immune system and can be leveraged for disease-specific targeting. These peptides are derived from intra-cellular proteins and ingested foreign antigens for presentation by class-I and class-II MHCs, respectively.
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Possu Huang Lab @possuhuanglab.bsky.social · 17/12/2024
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens TRACeR for MHC-I: go.nature.com/4gcLzn5 TRACeR for MHC-II: go.nature.com/4gj5OQk
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