ArticleMolecular systems biology2025
AlphaDesign: a de novo protein design framework based on AlphaFold.
Article in Molecular systems biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
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Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- HighFold4: extending AlphaFold3 to accurate cyclic peptide conformation prediction via custom chemical connectivity.Briefings in bioinformatics · 2026Article
- The structural chemistry and biosynthesis of chlorophylls.RSC chemical biology · 2026Review
- Efficient generation of epitope-targeted antibodies with Germinal.Nature biotechnology · 2026Article
- Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection.Nature communications · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Artificial intelligence driven protein design and sustainable nanomedicine for advanced theranostics.Bioactive materials · 2026Review
- ProtSeqGen: a novel deep learning model for protein sequence design.BMC bioinformatics · 2026Article
- Contemporary data-driven innovations in peptide-based therapeutic design.Briefings in bioinformatics · 2026Review
- Generative Protein Design: From Deep Learning Algorithms to Translational Applications.International journal of molecular sciences · 2026Review
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
- Review
- Generative design of synthetic gene circuits for functional and evolutionary properties.NPJ systems biology and applications · 2026Article
- AI-Driven Design of Miniproteins as Potential Allosteric Modulators.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms.Computational and structural biotechnology journal · 2026Review
- Architectural good practices for reproducible benchmarking in protein machine learning.Frontiers in bioinformatics · 2026Article
- Analysing open-source protein folding models for nanobody binding prediction.Frontiers in bioinformatics · 2026Article
- Designing novel solenoid proteins with in silico evolution.Communications chemistry · 2025Article
- Article
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Authors and funding
15 authors.
Funding
Abstract
De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.