AlphaFold2
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Related Articles from SNS
When Does Structure Help? The Information Bonus of AlphaFold2 Representations over Protein Language Models
arXiv:2606.04228v1 Announce Type: new Abstract: AI scientist systems increasingly choose biological foundation models before they choose experiments. In protein pipelines, this creates a concrete engineering and scientific question: when is the cost of structural inference worth paying over a cheaper sequence-only model? We introduce the information bonus (IB), a task-level metric that measures the linearly accessible advantage of frozen single-sequence AlphaFold2 Evoformer representations...
DeltaMut: An Integrative Database of AlphaFold2-Derived Missense Variant Structures
The widespread use of next-generation sequencing has led to a surge in the number of identified variants with uncertain effects on protein function. These variants pose a significant challenge in diagnostics and hinder patient treatment strategies. Numerous variant effect predictors (VEPs) are available to assess variant impact, but they primarily rely on sequence-derived information.
Do AI Structure Predictors Capture Bound-State Disorder? A Benchmark on Fuzzy Protein Complexes
Fuzzy protein complexes, in which an intrinsically disordered protein (IDP) retains conformational disorder upon binding, pose a fundamental challenge for structure predictors trained on ordered systems, where crystal structures capture only the most ordered ensemble snapshot, making standard benchmarking metrics misleading. Here, we present the first systematic evaluation of AlphaFold3 (AF3), AlphaFold2-Multimer (AF2MM), Chai-1, and Boltz-2 on a curated dataset of fuzzy complexes from...
The Unreasonable Redundancy of Nature's Protein Folds
The Unreasonable Redundancy of Nature's Protein Folds Over the last few years, deep neural networks have made generative language modeling dramatically more powerful, giving us large language models. A similar leap happened for continuous modalities like images and videos.
Mitochondria directly interact with the nuclear pore complex
Abstract Mitochondria regulate cellular processes through direct and indirect interactions with other organelles. A well-studied example has been contact with the endoplasmic reticulum at mitochondrial-associated endoplasmic reticulum membranes1, which control pathways including redox and calcium homeostasis2,3. Recent studies have also reported direct mitochondria–nuclear membrane contacts in cancer cells and yeast that promote pro-survival signalling4,5.
Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer
Abstract BRAF gain-of-function mutations, particularly BRAF(V600E), affect roughly 10% of all patients with colorectal cancer (CRC), and portend poor prognosis with limited therapeutic interventions. BRAF inhibitors such as encorafenib are ineffective due to MAPK pathway reactivation driven by BRAF dimerization. Combined inhibition of BRAF and EGFR, although approved therapies, results in short survival benefits and frequent treatment resistance and relapse1,2,3.