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PreprintU EdinburghProteins

Large-scale analysis of AlphaFold structures reveals organism-specific physicochemical signatures

Large-scale AlphaFold structure analysis reveals organism-specific physicochemical signatures reconstructed via DE-STRESS metrics across 48 proteomes and PDB structures.

Michael J. Stam

Published Oct 4, 2026 · 0 citations

100% Readers1 of 1 upvoted
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lenient 1/5
medium 3/10
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80%Must read
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arXivProteins

Learning Latent Protein Languages for Autoregressive Generation

Learned latent protein languages improve autoregressive generation scaling, speed, and quality versus amino-acid and coordinate token models.

Mahdi Pourmirzaei, Farzaneh Esmaili, Amir Ziashahabi, Mohammadreza Pourmirzaei and 1 more

Published Oct 2, 2026 · ▲ 5 on Hugging Face · Code

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AI panel: 12 of 20 reviewers recommend it
lenient 4/5
medium 8/10
strict 0/5
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NeurIPS 2026U CambridgeBigHat BiosciencesProteins

Bonobo: Efficient Library-Scale Generation for De Novo Antibody Design

Sebastian Ober, Nick Bhattacharya, Phillip M Maffettone, Calvin McCarter and 1 more

Sydney Poster Session 1, Tue, Dec 8, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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67%Highly rated
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NeurIPS 2026Inception AI4GoodIIAIProteins

Epitope-Conditioned Nanobody CDR Design via Retrieval-Augmented Protein Language Models

Mohammad Amaan Sayeed, Boulbaba Ben Amor

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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45%Niche pick
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NeurIPS 2026Max Planck Institute of BiochemiMax Planck Institute for BiochemHKUST-GZETH ZurichLudwig-Maximilians-Universität MProteins

Joint protein, mRNA, DNA sequence design and optimization with nucleotide-level Potts models

Blazej Banaszewski, Lars J Dornfeld, Dexiong Chen, Karsten Borgwardt and 1 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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67%Highly rated
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NeurIPS 2026Shanghai JiaotongShanghai Jiao TongProteins

Energy-Adaptive Equivariant State Space Models for Noise-Robust Protein Structure Representation

Zhongyue Zhang, Runze Ma, Yanjie Huang, Shuangjia Zheng

Sydney Poster Session 4, Wed, Dec 9, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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57%Worth a look
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NeurIPS 2026UCLAU California, Los AngelesU California, San DiegoProteins

Efficient and Accurate Zero Shot Generation of Symmetric Protein Complexes

Rory Gao, Yuanzhou Chen, Prajit Rajkumar, Wei Wang

Sydney Poster Session 3, Wed, Dec 9, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Queen Mary, University of LondonSyngenta AGSyngentaProteins

PaxBench: A Multimodal Sequence Benchmark for Protein Abundance Prediction

Ke Zhai, Oscar J Charles, Helena A Saunders, Conrad Bessant

Sydney Poster Session 5, Thu, Dec 10, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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NeurIPS 2026Universität des SaarlandesPrescient Design & UniversitF. Hoffmann-La Roche Ltd.Prescient DesignProteins

Can Folding Models Tell Binders from Bluffers? Evidence from POISK: The Patent-Derived Antibody Dataset

Daria Tupikina, Andrea Roncoli, Alexander Bujotzek, Brennan Abanades Kenyon

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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67%Highly rated
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NeurIPS 2026U Science and Technology of ChinAnew therapeuticsAnt GroupSouthern University of Science aPekingProteins

FoldAbS: Repurposing the Protein Folding Model as a Foundation Encoder for Antibody Screening

Jun Wu, FANDI WU, Xinyuan Zhu, Dawei Huang and 4 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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lenient 2/5
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67%Highly rated
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NeurIPS 2026U Illinois ChicagoU Illinois at ChicagoProteins

MSConsensus: A Hundred-Million-Scale, Batch-Effect–Suppressed Dataset and Benchmark for Proteomics Machine Learning

Christopher Grams, Chang Liu, Michael Papka, Yu Gao

Atlanta Poster Session 1, Wed, Dec 9, 10:00 AM–1:00 PM, Hall C1 · Published 2026

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lenient 1/5
medium 0/10
strict 1/5
67%Highly rated
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NeurIPS 2026ShanghaiTechProteins

CryoAtlas: A Large Curated Dataset and Unified Benchmark for Cryo-EM Atomic Model Building

Mingrui Li, Minzhang Li, Weichen Qin, Yufan Xie and 5 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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lenient 1/5
medium 0/10
strict 1/5
67%Highly rated
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NeurIPS 2026StanfordU Maryland, College ParkImperial College LondonGoogle DeepMindProteins

Plausible Biomolecular Structure Prediction via Physics-informed Reinforcement Learning

Tai Dang, Hieu Tran, Long-Hung Pham, Sang Truong and 3 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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lenient 2/5
medium 0/10
strict 0/5
57%Worth a look
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NeurIPS 2026StanfordProxy FoodsU PiraeusProxy Foods Inc.Food System InnovationsProteins

Expert-guided Bayesian optimization for sustainable protein formulation

Anna Thomas, Georgios Zaverdinos, Petros Mandalis, Andreas Orfanoudakis and 8 more

Sydney Poster Session 6, Thu, Dec 10, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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lenient 1/5
medium 0/10
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45%Niche pick
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NeurIPS 2026The University of Texas at AustiSapienza university of RomeGoogle DeepMindU Texas, AustinSapienza University of RomeProteins

Anchored Protein Engineering

Chi Zhang, Maria Rosaria Briglia, Litu Rout, Jeffrey Ouyang-Zhang and 4 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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70%Highly rated
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NeurIPS 2026UC BerkeleyMicrosoftMicrosoft ResearchProteins

Bigger Isn’t Better: Why the Indiscriminate Scaling of Foundation Models Can’t Solve Biology

Kathryne Metcalf, Lorin Crawford, Mary L Gray, Kevin K Yang and 1 more

Sydney Poster Session 2, Tue, Dec 8, 5:00 PM–8:00 PM, Hall 1-4 · Published 2026

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lenient 2/5
medium 1/10
strict 1/5
57%Worth a look
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NeurIPS 2026Carnegie MellonCMU, Carnegie MellonU WashingtonStanfordProteins

DUIL: Deep Unsupervised Inverse Learning for in situ Macromolecular Morphology Identification

Mostofa Rafid Uddin, Seonghui Min, Mahek Vora, Qifeng Wu and 2 more

Atlanta Poster Session 2, Wed, Dec 9, 4:30 PM–7:30 PM, Hall C1 · Published 2026

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lenient 1/5
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NeurIPS 2026Dalian University of TechnologyProteins

KnowEvo: Knowledge Evolution for Protein Optimization

Zijie Xing, Xingyue Liu, Runze Wang, Luoming Hu and 1 more

Paris Poster Session 1, Wed, Dec 9, 12:30 PM–2:30 PM, Paris Poster Hall · Published 2026

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NeurIPS 2026VanderbiltProteins

Benchmarking sequence-to-ensemble predictors on UNICORNEdb, a UniProt-grouped database of PDB-derived conformational ensembles

William F Vanderbilt-Fried, Luka Butskhrikidze, Benjamin P Brown, Hassane Mchaourab and 1 more

Paris Poster Session 1, Wed, Dec 9, 12:30 PM–2:30 PM, Paris Poster Hall · Published 2026

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83%Must read
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NeurIPS 2026U California, BerkeleyUC BerkeleyProteins

Spectral Feedback for Test-Time Alignment of Protein Diffusion Models

Spectral Feedback iteratively selects protein tokens to re-mask and resample using sparse Fourier edit-set value functions, improving inverse-folding stability by up to 32.3% at test time.

Shai Dickman, Mert Cemri, Landon Butler, Kannan Ramchandran

Sydney Poster Session 3, Wed, Dec 9, 10:00 AM–1:00 PM, Hall 1-4 · Published 2026

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AI panel: 13 of 20 reviewers recommend it
lenient 5/5
medium 7/10
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