FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila www.biorxiv.org/cont...

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#proteomics #prot-preprint

FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila

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FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila [new]

FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila www.biorxiv.org/content/10.64898/2026.04...

Experimental assessment of AI-based interactome mapping
www.nature.com/articles/s41...

A Constrained Degron Tag Engineered to Enhance Auxin-Inducible Protein Degradation The auxin-inducible degron (AID) system enables targeted protein degradation in vivo. Conventionally, the AID tag is fused directly to the terminus of the target protein; however, its intrinsically di...

A Constrained Degron Tag Engineered to Enhance Auxin-Inducible Protein Degradation
pubs.acs.org/doi/10.1021/...

Charged molecular glue discovery enabled by targeted degron display www.nature.com/articles/s41...

Compressing the collective knowledge of ESM into a single protein language model - Nature Methods A co-distillation framework is used to iteratively adapt sequence-only protein language models for high-accuracy variant effect prediction, without the need for additional structural or genetic data. ...

Compressing the collective knowledge of ESM into a single protein language model

www.nature.com/articles/s41...

Atlas of predicted protein complex structures across kingdoms

www.nature.com/articles/s41...

The E3-ome gene-centric compendium reveals the human E3 ligase landscape The E3-ome defines the human repertoire of ubiquitin E3 ligases, creating a unified resource that maps their diversity across the ubiquitin and ubiquitin-like systems. By consolidating fragmented know...

The E3-ome gene-centric compendium reveals the human E3 ligase landscape
www.cell.com/cell/fulltex...

Organization of neuropeptide systems in the human brain - Nature Neuroscience This study comprehensively maps neuropeptide systems in the human brain to elucidate their organizational principles and shows how neuropeptide architecture is linked to behavior and evolution.

Organization of neuropeptide systems in the human brain

www.nature.com/articles/s41...

Single-molecule peptide sequencing through reverse translation of peptides into DNA - Nature Biotechnology Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.

Single-molecule peptide sequencing through reverse translation of peptides into DNA

www.nature.com/articles/s41...

Autophagolysosomal exocytosis inverts Src kinase onto the cell surface in cancer Overexpression of the proto-oncogene Src is common to a wide variety of cancers. In this work, we found that Src is noncanonically translocated and inverted onto the cell surface in cancer, both in vi...

Autophagolysosomal exocytosis inverts Src kinase onto the cell surface in cancer
www.science.org/doi/10.1126/...

Endocytome profiling uncovers cell-surface protein dynamics underlying neuronal connectivity Endocytome profiling is a powerful approach to decode rapid remodeling of the cell-surface proteome across cell states and contexts in intact tissues. Applying this tool to developing axons, McLaughli...

Endocytome profiling uncovers cell-surface protein dynamics underlying neuronal connectivity
www.cell.com/neuron/fullt...

How somatic evolution affects health - Nature Ecology & Evolution As somatic evolution becomes directly measurable, integrating eco-evolutionary principles with high-resolution molecular data creates opportunities to anticipate and prevent disease.

How somatic evolution affects health

www.nature.com/articles/s41...

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2 - Nature Methods AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments, homology models or knowled...

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2

www.nature.com/articles/s41...

A proteome-wide dependency map of protein interaction motifs - Nature Structural & Molecular Biology Ambjørn and Meeusen et al. functionally characterize all reported and a comprehensive set of predicted short linear motifs (SLiMs) using base-editing screens, identifying 450 reported and 264 predicte...

A proteome-wide dependency map of protein interaction motifs
www.nature.com/articles/s41...

I’ll be presenting FlyPredictome (1.7M+ predictions!) on Saturday evening at #dros26. Whether you're into the Secretome, Kinases, or Phenotype-to-interactomes, come see how this atlas can power your biology! 🪰🧬

Flypredictome: www.flyrnai.org/tools/fly_pr...
Github: github.com/flyark/AFM-LIS

Recent discoveries on the acquisition of the highest levels of human performance Scientists have long debated the origins of exceptional human achievements. This literature review summarizes recent evidence from multiple domains on the acquisition of world-class performance. We re...

Multidisciplinary training, over time, produces the highest impact people

www.science.org/doi/10.1126/...

qMaLioffG: a genetically encoded green fluorescence lifetime-based indicator enabling quantitative imaging of intracellular ATP
#Drosophila

A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome www.biorxiv.org/content/10.1101/2025.10....

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A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome [new]
Kinase docking on TFs predicted; novel homeodomain motif found.

Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer Paraneoplastic syndromes arise when tumor-derived cytokines reprogram distant organs. Although mediators such as Interleukin-6 have been implicated, how these signals impair host organ function remain...

New paper: Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer
Liu, Miao, Wang, Ezequiel, Kim, Zhang, Sun, Binari, Asara, Yanhui Hu, Goncalves, Janowitz, Perrimon
doi: doi.org/10.1101/2025...

A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome Protein kinases orchestrate cellular processes through phosphorylation, yet the structural basis for their specific binding partner interactions remains largely unmapped. Here, we present a structure-...

New paper: A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome
Kim, Huang, Johnson, Yaron-Barir, Keven Wang, Cantley, Hu, Perrimon
bioRxiv 2025.10.10.681672; doi: doi.org/10.1101/2025...

New research from Dana-Farber Cancer Institute

A new study in @cp-molcell.bsky.social by @danafarber.bsky.social’s Mikołaj Słabicki, PhD, Benjamin Ebert, MD, PhD, and Eric Fischer, PhD, reports a systematic screen of 9,000 zinc fingers revealing 38 new CRBN-recruited degrons, expanding the ZF proteome map to guide drug design. bit.ly/41XoG1Q

Dear Fly Community, In May 2025, the NIH terminated all grant funding to Harvard University, including the NHGRI grant that supported FlyBase. This grant also funded FlyBase teams at Indiana University (IU) and the University of Cambridge (UK), and as a result, their subawards were also canceled. The Cambridge team has secured support for one to two years through generous donations from the European fly community, emergency funding from the Wellcome Trust, and support from the University of Cambridge. At IU, funding has been secured for one year thanks to reserve funds from Thom Kaufman and a supplement from ORIP/NIH to the Bloomington Drosophila Stock Center (BDSC). Unfortunately, the situation at Harvard is far more critical. Harvard University had supported FlyBase staff since May but recently denied a request for extended bridge funding. As a result, all eight employees (four full-time and four part-time) were abruptly laid off, with termination dates ranging from August to mid-October depending on their positions. In addition, our curator at the University of New Mexico will leave her position at the end of August. This decision came as a shock, and we are urgently pursuing all possible funding options. To put the need into perspective: although FlyBase is free to use, it is not free to make. It takes large teams of people and millions of dollars a year to create FlyBase to support fly research (the last NHGRI grant supported us with more than 2 million USD per annum). To help sustain FlyBase operations, we have been reaching out to you to ask for your support. We have set up a donation site in Cambridge, UK, to which European labs have and can continue to contribute, and a new donation site at IU to which labs in the US and the rest of the world can contribute. We urge researchers to work with their grant administrators to contribute to FlyBase via these sites if at all possible, as more of the money will go to FlyBase. However, we appreciate that some fu…

https://wiki.flybase.org/wiki/FlyBase:Contribute_to_FlyBase Our immediate goals are: 1. To maintain core curation activities and keep the FlyBase website online 2. To complete integration with the Alliance of Genome Resources (The Alliance). Integration with the Alliance is essential for FlyBase’s long-term sustainability. For nearly a decade, NHGRI/NIH has supported the unification of Model Organism Databases (MODs) into the Alliance, which we aim to achieve by 2028. Therefore, securing bridge funding to sustain FlyBase over the next three years is crucial for successful integration and the long-term access to FlyBase data. At present, our remaining funds will allow us to keep the FlyBase website online for approximately one more year. Beyond that, its future is uncertain unless new funding is secured. We will, of course, continue pursuing additional grant opportunities as they arise. Given the uncertainty of future NIH or alternative funding sources, we are relying on the Fly community for support. Your contributions will directly help us retain the staff needed to complete this transition and to secure ongoing fly data curation into the Alliance beyond 2028. We at FlyBase are incredibly grateful for the outpouring of support from the community during this challenging time. Your encouragement has strengthened our resolve and underscores how vital this resource remains to Drosophila research worldwide. Sincerely, The FlyBase Team

The community of Drosophila researchers is amazing, mutually supportive and collaborative. Right now a key resource for our community, @flybase.bsky.social , is threatened by the cancellation of its NIH grant and is seeking community help in raising short term funds 1/n 🧪 please share

FlyBase needs your help! We ask that European labs continue to contribute to Cambridge, UK FlyBase, whereas US and other non-European labs can contribute to US FlyBase. For more information and how to donate: wiki.flybase.org/wiki/FlyBase...

Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking Secreted proteins regulate many aspects of animal biology and are attractive targets for biomarkers and therapeutics. However, comprehensively identifying the "secretome", along with their tissues of ...

I’m thrilled to share a @biorxivpreprint for my postdoc work in the @PerrimonLab🎉. Together with our collaborators, we built a tissue-specific atlas of circulating secreted proteins in Drosophila 🧬🪰🧪🗺️.
Thread below🧵
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www.biorxiv.org/content/10.1...

FlyPhoneDB2: A Computational Framework for Analyzing Cell-Cell Communication in Drosophila scRNA-seq Data Integrating AlphaFold-Multimer Predictions Cell-cell communication (CCC) plays a critical role in the physiological regulation of organisms and has been implicated in numerous diseases. Previously, we introduced FlyPhoneDB, a tool designed to ...

FlyPhoneDB2: A Computational Framework for Analyzing Cell-Cell Communication in Drosophila scRNA-seq Data Integrating AlphaFold-Multimer Predictions
www.csbj.org/article/S200...

Measuring the value and impact of UniProt Case study shows the economic value and impact of UniProt, showing estimated annual gains of up to €5,475 per user.

New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information.

Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.

www.ebi.ac.uk/about/news/a...

xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins - Nature Methods xTrimo protein general language model (xTrimoPGLM) is a unified pretraining framework and foundation model designed for various protein-related tasks, including protein understanding and generation or...

xTrimoPGLM: unified 100-billion-parameter pretrained transformer for deciphering the language of proteins
www.nature.com/articles/s41...