ArticleBioinformatics advances2024
Accelerating protein-protein interaction screens with reduced AlphaFold-Multimer sampling.
Article in Bioinformatics advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- AlphaFold reveals how pathogenicmBio · 2026Article
- Targeting protein protein interactions and their modulators to enable new therapeutic strategies for human diseases.NPJ systems biology and applications · 2026Review
- Analysing open-source protein folding models for nanobody binding prediction.Frontiers in bioinformatics · 2026Article
- AstraMEV (AI-Guided Structural Assembly of Multi-Epitope Vaccines) Against Infectious Bronchitis Virus.Journal of chemical information and modeling · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- A new age in structural S-layer biology: Experimental and in silico milestones.The Journal of biological chemistry · 2025Review
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Multidimensional analysis reveals gene expression, cell interactions, and signaling networks in glioma and Alzheimer's disease.Discover oncology · 2025Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Discovering new protein-protein interactions (PPIs) across entire proteomes offers vast potential for understanding novel protein functions and elucidate system properties within or between an organism. While recent advances in computational structural biology, particularly AlphaFold-Multimer, have facilitated this task, scaling for large-scale screenings remains a challenge, requiring significant computational resources. Results: We evaluated the impact of reducing the number of models generated by AlphaFold-Multimer from five to one on the method's ability to distinguish true PPIs from false ones. Our evaluation was conducted on a dataset containing both intra- and inter-species PPIs, which included proteins from bacterial and eukaryotic sources. We demonstrate that reducing the sampling does not compromise the accuracy of the method, offering a faster, efficient, and environmentally friendly solution for PPI predictions. Availability and implementation: The code used in this article is available at https://github.com/MIDIfactory/AlphaFastPPi. Note that the same can be achieved using the latest version of AlphaPulldown available at https://github.com/KosinskiLab/AlphaPulldown.
Identifiers
What OpenQuestion holds
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.