Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling v...

The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity i...

SUMOylation is an essential eukaryotic ubiquitin-like post-translational modification that plays a central role in the regulation of various nuclear processes and stress responses. It canonically occu...

Short linear motifs (SLiMs) within intrinsically disordered protein regions mediate transient interactions crucial for cell physiology. However, the global interaction landscape of human SLiMs remains...

Folddisco enables protein structural motif search in million scale databases.

PPIscreenML is a rigorously benchmarked method that uses AlphaFold2 to screen for interacting protein pairs, and it provides superior performance to other available methods.

Ubiquitin coordinates a complex network of cellular pathways through covalent modification of substrates. Specificity in substrate recognition and modification choice is largely conferred by ubiquitin...

Ubiquitin (Ub) cooperation with other post-translational modifications provides a tiered opportunity for protein regulation. Small modifications to Ub such as phosphorylation, acetylation, or ADP-ribo...

Squair et al. show that ZNFX1 restricts ssRNA virus replication by integrating SF1 helicase activity with dual E3 ligase mechanisms. ATP-dependent RNA binding activates E3 function, driving self-propa...

imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

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 knowledge, this framework provides a foundation for studying ubiquitin signaling and accelerating discovery.

SUMOylation is a post-translational modification catalyzed by a multi-step enzymatic cascade. To gain structural biology insights into the last step of this process, where SUMO is transferred from a S...

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,...

Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...

The ubiquitin system is fundamental to virtually all biological processes and is essential for maintaining cellular and organismal homeostasis. Recent technological advances are revealing new roles f…

Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

Protein scientists could improve reproducibility and coordination across the field by rallying around a small, shared set of "model proteins," according to a new Perspective by Connecticut College che...

Recent breakthroughs in protein structure prediction have opened new avenues for genome-wide drug discovery, yet existing virtual screening methods remain computationally prohibitive. We present DrugC...

YouTube video by David Fay

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.