ArticlePLoS computational biology2024
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families.BioData mining · 2026Review
- AlphaFold-Multimer modelling of linked nAChR subunits challenges concatemer design assumptions.Scientific reports · 2026Article
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- AI-aided engineering and production optimization of chimeric hetero-viral capping enzymes for mRNA vaccines.Scientific reports · 2026Article
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
- Article
- A novel anti-Microbiology spectrum · 2026Article
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- Recombinant collagen in regenerative medicine: Expression strategies, structural design, and translational applications.Materials today. Bio · 2025Review
- Xtricorder: a likelihood-enhanced self-rotation function and application to a machine learning-enhanced Matthews prediction of asymmetric unit copy number.Acta crystallographica. Section D, Structural biology · 2025Article
- Computer-Aided Drug Design Across Breast Cancer Subtypes: Methods, Applications and Translational Outlook.International journal of molecular sciences · 2025Review
- Training bias and sequence alignments shape protein-peptide docking by AlphaFold and related methods.Protein science : a publication of the Protein Society · 2025Article
- Investigating whether deep learning models for co-folding learn the physics of protein-ligand interactions.Nature communications · 2025Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
- Selective disruption of DNMT1/ELK1 interactions induces DGKI re-expression and promotes temozolomide sensitivity of MGMTClinical epigenetics · 2025Article
- A new age in structural S-layer biology: Experimental and in silico milestones.The Journal of biological chemistry · 2025Review
- Identification of the Plant Defensin (MsPDF) Gene Family inPlants (Basel, Switzerland) · 2025Article
- Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction.PLoS computational biology · 2025Article
- DET1 dynamics underlie cooperative ubiquitination by CRL4Science advances · 2025Article
- Fibrotic lung ECM upregulates SDC4/integrin-αvβ1 interaction and the interfering peptide SDC4Regenerative biomaterials · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
Structure prediction of protein complexes has improved significantly with AlphaFold2 and AlphaFold-multimer (AFM), but only 60% of dimers are accurately predicted. Here, we learn a bias to the MSA representation that improves the predictions by performing gradient descent through the AFM network. We demonstrate the performance on seven difficult targets from CASP15 and increase the average MMscore to 0.76 compared to 0.63 with AFM. We evaluate the procedure on 487 protein complexes where AFM fails and obtain an increased success rate (MMscore>0.75) of 33% on these difficult targets. Our protocol, AFProfile, provides a way to direct predictions towards a defined target function guided by the MSA. We expect gradient descent over the MSA to be useful for different tasks.
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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.