ArticleNature communications2024
Modelling protein complexes with crosslinking mass spectrometry and deep learning.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Predicting RNA and Protein:RNA Complexes with AlphaFold: Possibilities, Limitations, and Practical Guidelines.Methods in molecular biology (Clifton, N.J.) · 2027Article
- The phenotypic landscape of the model firmicuteProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evaluation of methods for AlphaFold-based integrative modeling.bioRxiv : the preprint server for biology · 2026Article
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- Novel Insights into the Human Hsc70 Structure by Cross-Linking Mass Spectrometry and Molecular Modeling.Journal of proteome research · 2026Article
- Synthetic sequence alignments as programmable probes of learned conformational landscapes in deep learning protein structure predictors.Bioinformatics (Oxford, England) · 2026Article
- Regulation of iron ion homeostasis inmBio · 2026Review
- Interface swapping orchestrates carbon transfer in the archaeal acetyl-CoA decarbonylase/synthase.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive Tutorial for Computational Methods of Protein Structure Prediction Incorporating Mass Spectrometry Data.Mass spectrometry reviews · 2026Review
- Complete enzyme clustering enhances coenzyme Q biosynthesis via substrate channeling.Nature communications · 2026Article
- PMGen: from peptide-MHC structure prediction to peptide generation.Bioinformatics (Oxford, England) · 2026Article
- Bridging structure and function: artificial intelligence-based modelling of kidney proteins.Nature reviews. Nephrology · 2026Review
- Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.bioRxiv : the preprint server for biology · 2026Article
- Inherent MS-cleavability of diazirine photo-cross-links enables residue-level structural analysis.Nature communications · 2026Article
- Assembly of two functionally-distinct protein import complexes in the outer membrane of plant chloroplasts.Nature communications · 2026Article
- RPA directly stimulates Mer3 helicase processivity to ensure normal crossover formation in meiosis.Nature communications · 2026Article
- Histone 3 lysine 9 dimethylation by the G9a-GLP heterodimer requires intranucleosomal product reading.bioRxiv : the preprint server for biology · 2026Article
- Guiding AlphaFold predictions with experimental knowledge to inform dynamics and interactions with VAIRO.Protein science : a publication of the Protein Society · 2026Article
- Cryo-EM structure of the vaccinia virus entry fusion complex reveals a multicomponent fusion machinery.Science advances · 2026Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrate experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially improves modelling performance on challenging targets, by helping to identify interfaces, focusing sampling, and improving model selection. This extends to single crosslinks from whole-cell crosslinking MS, opening the possibility of whole-cell structural investigations driven by experimental data. We demonstrate this by revealing the molecular basis of iron homoeostasis in Bacillus subtilis.
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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.