Combined pooled-AlphaFold3 PPI prediction and high-throughput genomics approach is established as the gold standard for large-scale characterization of protein function.
A high-coverage crosslinking mass spectrometry framework is developed to map the proteome-wide interactome of the model apicomplexan parasite Toxoplasma gondii and identifies and validated previously unrecognized components of essential protein complexes, including a structurally distinct ATP synthase subcomplex contai...
S. Butterworth, Ashley L. Gin, Shikha Shikha et al.· bioRxiv· 0 citations
MitoMatch is presented, an AlphaFold Multimer-based compendium of mitochondrial protein interactions that links orphan proteins to known pathways, defines the CoQ metabolon, and reveals the role of COA4 in copper delivery to cytochrome c oxidase.
Abhinav B. Swaminathan, M. Zulkifli, Rachel M. Guerra et al.· Nature Communications· 0 citations
HInt (Homology by Interaction), an accelerated AlphaFold-based framework that enables practical proteome-scale PPI prediction through biologically informed pre-filtering and optimised high-throughput structure modelling, and provides a general framework for uncovering hidden homologues and expands the conceptual landsc...
Quentin Rouger, P. Paillard, Manon Thomet et al.· bioRxiv· 0 citations
A systematic computational workflow is presented for the identification and structural analysis of putative effector proteins in Ustilago maydis, a biotrophic model fungus, providing a framework to prioritize effector candidates for experimental validation and can be readily applied to diverse fungal pathogens.
Max Heinen, Florian Altegoer· Methods in molecular biology· 0 citations
Functional screening is extended into a lineage of actinobacteriophages that has not previously been characterized, and several proteins with no known function are identified that warrant further mechanistic analysis.
A. Tennakoon, I. Edirisingha, Cole R. Jirsa et al.· G3· 0 citations
GenomeProt, a user-friendly GUI-based tool for integrative proteogenomic analysis, is developed and demonstrated its utility by integrating long-read RNA sequencing with mass-spectrometry-based proteomics to pinpoint proteoform expression generated by alternative splicing.
Hitesh Kore, Josie Gleeson, C. Wan et al.· bioRxiv· 1 citation
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