On fine-tuning Boltz-2 for protein-protein affinity prediction
Fuente:
arXiv
Saved in:
| Main Authors: | King, James, Cornwall, Lewis, Nica, Andrei Cristian, Day, James, Sim, Aaron, Dalchau, Neil, Wollman, Lilly, Meyers, Joshua |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Sequence-based protein-protein interaction prediction and its applications in drug discovery
by: Charih, François, et al.
Published: (2025)
by: Charih, François, et al.
Published: (2025)
Persistent local Laplacian prediction of protein-ligand binding affinities
by: Liu, Jian, et al.
Published: (2026)
by: Liu, Jian, et al.
Published: (2026)
Assessing interaction recovery of predicted protein-ligand poses
by: Errington, David, et al.
Published: (2024)
by: Errington, David, et al.
Published: (2024)
Mayer-homology learning prediction of protein-ligand binding affinities
by: Feng, Hongsong, et al.
Published: (2024)
by: Feng, Hongsong, et al.
Published: (2024)
Multiscale guidance of protein structure prediction with heterogeneous cryo-EM data
by: Raghu, Rishwanth, et al.
Published: (2025)
by: Raghu, Rishwanth, et al.
Published: (2025)
On diffusion posterior sampling via sequential Monte Carlo for zero-shot scaffolding of protein motifs
by: Young, James Matthew, et al.
Published: (2024)
by: Young, James Matthew, et al.
Published: (2024)
CAML: Commutative algebra machine learning -- a case study on protein-ligand binding affinity prediction
by: Feng, Hongsong, et al.
Published: (2025)
by: Feng, Hongsong, et al.
Published: (2025)
DisorderUnetLM: Validating ProteinUnet for efficient protein intrinsic disorder prediction
by: Kotowski, Krzysztof, et al.
Published: (2024)
by: Kotowski, Krzysztof, et al.
Published: (2024)
ProtFAD: Introducing function-aware domains as implicit modality towards protein function prediction
by: Wang, Mingqing, et al.
Published: (2024)
by: Wang, Mingqing, et al.
Published: (2024)
Towards protein folding pathways by reconstructing protein residue networks with a policy-driven model
by: Khor, Susan
Published: (2026)
by: Khor, Susan
Published: (2026)
De novo design of high-affinity protein binders with AlphaProteo
by: Zambaldi, Vinicius, et al.
Published: (2024)
by: Zambaldi, Vinicius, et al.
Published: (2024)
Exploring zero-shot structure-based protein fitness prediction
by: Sharma, Arnav, et al.
Published: (2025)
by: Sharma, Arnav, et al.
Published: (2025)
One protein is all you need
by: Bushuiev, Anton, et al.
Published: (2024)
by: Bushuiev, Anton, et al.
Published: (2024)
Evaluating representation learning on the protein structure universe
by: Jamasb, Arian R., et al.
Published: (2024)
by: Jamasb, Arian R., et al.
Published: (2024)
Aptamer-protein interaction prediction model based on transformer
by: Yan, Zhichao, et al.
Published: (2025)
by: Yan, Zhichao, et al.
Published: (2025)
Representation choice shapes the interpretation of protein conformational dynamics
by: Giottonini, Axel, et al.
Published: (2026)
by: Giottonini, Axel, et al.
Published: (2026)
Learning residue level protein dynamics with multiscale Gaussians
by: Bafna, Mihir, et al.
Published: (2025)
by: Bafna, Mihir, et al.
Published: (2025)
Kermut: Composite kernel regression for protein variant effects
by: Groth, Peter Mørch, et al.
Published: (2024)
by: Groth, Peter Mørch, et al.
Published: (2024)
AlphaFold2 for protein structure prediction: Best practices and critical analyses
by: Radjasandirane, Ragousandirane, et al.
Published: (2024)
by: Radjasandirane, Ragousandirane, et al.
Published: (2024)
Inference-time optimization for experiment-grounded protein ensemble generation
by: Maddipatla, Advaith, et al.
Published: (2026)
by: Maddipatla, Advaith, et al.
Published: (2026)
Predicting mutational effects on protein binding from folding energy
by: Deng, Arthur, et al.
Published: (2025)
by: Deng, Arthur, et al.
Published: (2025)
Fold-switching proteins push the boundaries of conformational ensemble prediction
by: Lee, Myeongsang, et al.
Published: (2026)
by: Lee, Myeongsang, et al.
Published: (2026)
Quantification of protein homodimer affinity using native mass spectrometry
by: Schulte, Jonathan, et al.
Published: (2025)
by: Schulte, Jonathan, et al.
Published: (2025)
ProteinGuide: On-the-fly property guidance for protein sequence generative models
by: Xiong, Junhao, et al.
Published: (2025)
by: Xiong, Junhao, et al.
Published: (2025)
Mask prior-guided denoising diffusion improves inverse protein folding
by: Bai, Peizhen, et al.
Published: (2024)
by: Bai, Peizhen, et al.
Published: (2024)
Physical principles of building protein megacomplexes in a crowded milieu
by: Wang, Jiayi, et al.
Published: (2026)
by: Wang, Jiayi, et al.
Published: (2026)
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation
by: Frellsen, Jes, et al.
Published: (2025)
by: Frellsen, Jes, et al.
Published: (2025)
MotifBench: A standardized protein design benchmark for motif-scaffolding problems
by: Zheng, Zhuoqi, et al.
Published: (2025)
by: Zheng, Zhuoqi, et al.
Published: (2025)
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
by: Didi, Kieran, et al.
Published: (2023)
by: Didi, Kieran, et al.
Published: (2023)
Conditioned free-energy density of proteins using unbalanced solutions to constraint satisfaction problems
by: Worah, Pratik, et al.
Published: (2026)
by: Worah, Pratik, et al.
Published: (2026)
Identifying critical residues of a protein using meaningfully-thresholded Random Geometric Graphs
by: Zhang, Chuqiao, et al.
Published: (2025)
by: Zhang, Chuqiao, et al.
Published: (2025)
Assessment of scoring functions for computational models of protein-protein interfaces
by: Sumner, Jacob, et al.
Published: (2024)
by: Sumner, Jacob, et al.
Published: (2024)
GenShin:geometry-enhanced structural graph embodies binding pose can better predicting compound-protein interaction affinity
by: Zhu, Pingfei, et al.
Published: (2025)
by: Zhu, Pingfei, et al.
Published: (2025)
ENSEMBITS: an alphabet of protein conformational ensembles
by: Shi, Kaiwen, et al.
Published: (2026)
by: Shi, Kaiwen, et al.
Published: (2026)
Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids
by: Ferraz, Lucas, et al.
Published: (2026)
by: Ferraz, Lucas, et al.
Published: (2026)
In silico bioactivity prediction of proteins interacting with graphene-based nanomaterials guides rational design of biosensor
by: Ye, Jing, et al.
Published: (2024)
by: Ye, Jing, et al.
Published: (2024)
State-aware protein-ligand complex prediction using AlphaFold3 with purified sequences
by: Xing, Enming, et al.
Published: (2025)
by: Xing, Enming, et al.
Published: (2025)
Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction
by: Chakravarty, Devlina, et al.
Published: (2024)
by: Chakravarty, Devlina, et al.
Published: (2024)
Transformer-based toxin-protein interaction analysis prioritizes airborne particulate matter components with potential adverse health effects
by: Zhu, Yan, et al.
Published: (2024)
by: Zhu, Yan, et al.
Published: (2024)
FoldToken2: Learning compact, invariant and generative protein structure language
by: Gao, Zhangyang, et al.
Published: (2024)
by: Gao, Zhangyang, et al.
Published: (2024)
Similar Items
-
Sequence-based protein-protein interaction prediction and its applications in drug discovery
by: Charih, François, et al.
Published: (2025) -
Persistent local Laplacian prediction of protein-ligand binding affinities
by: Liu, Jian, et al.
Published: (2026) -
Assessing interaction recovery of predicted protein-ligand poses
by: Errington, David, et al.
Published: (2024) -
Mayer-homology learning prediction of protein-ligand binding affinities
by: Feng, Hongsong, et al.
Published: (2024) -
Multiscale guidance of protein structure prediction with heterogeneous cryo-EM data
by: Raghu, Rishwanth, et al.
Published: (2025)