protein folding

Chromo domain proteins: Forms and functions

ProDiPA: Offline Multi-Teacher Distillation and Pareto Alignment for Protein Generation

Overview. This Zenodo record is the compact public-release view of the UniRef50-MultiProp (U50-MP) dataset: a homology-partitioned protein sequence collection with predicted structural confidence, solubility, and thermophilic propensity annotations. It does not rebuild, re-filter, re-cluster, re-split, or re-score any...

Ultrathin Protein Films Create Living Catalytic Interfaces on Microbial Cells

Spatial organization underpins efficient multistep catalysis in nature, yet recreating such organization on living cell surfaces using mild, enzyme-compatible and catalytically functional materials remains challenging. Here we report an l-cysteine-triggered silk fibroin/lysozyme ultrathin film (SLF) that assembles di...

Integrating physiological and proteomics signatures for understanding drought, salinity and alkalinity stress tolerance mechanisms in lentil

Abiotic stresses—such as drought, salinity, and alkalinity severely limit global lentil production by impairing physiological processes including osmolytes accumulation, chlorophyll synthesis, H 2 O 2 production and antioxidant activities. However, no proteomic signature studies have dissected the molecular mechanisms...

Graph Neural Network Modelling of Pre-Diagnostic Serum Proteomics for Pancreatic Cancer Detection

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) has exceptionally high mortality, largely because of late diagnosis, while established blood biomarkers such as CA19-9 have limited sensitivity for early detection. We evaluated whether modelling serum proteomic measurements as supervised pairwise statistic...

FlexENN: A Graph Neural Network for Binding Energy Prediction of Globular and Intrinsically Disordered Proteins

Abstract Intrinsically disordered proteins (IDPs) drive a large fraction of cellular signaling, transcription, and assembly through interfaces that often lack a defined geometry, making the prediction of their binding energies challenging for methods developed primarily for folded complexes. Here, we introduce FlexENN,...

Clinical and molecular insights into primary ciliary dyskinesia: Genotype-phenotype correlation and protein interaction networks in an Indian retrospective cohort.

Understanding of PCD variants in the Indian population is enhanced and the value of combining clinical evaluations with genomic and structural analyses is highlighted, as PPI and GO analyses reveal disrupted ciliary pathways linked to PCD.

Probing transcript RNA G-quadruplexes using an engineered RHAU-RNase HI enzyme.

G-quadruplexes (G4s) in functional RNAs regulate telomere maintenance, mRNA processing, and disease pathways, but their detection in long transcripts is limited by biophysical methods. Herein, we engineered RHAU-RNase HI, fusing the G4-binding RHAU domain (aa 53-192) with RNase HI (Bacillus halodurans), to probe RNA G4...

Recurrent catalytic-site change and electrostatic remodeling across the HEPN ribonuclease fold.

Together, these results establish recurrent catalytic-state change and physicochemical remodeling of the ancestral HEPN cleft, whether such remodeling corresponds to altered binding, regulation, or another molecular function remains a hypothesis requiring experimental testing.

KPTM-MCHR: A multichannel hypergraph regression model for predicting the frequencies of lysine post-translational modification types in proteins.

This study presents a pioneering model for predicting the frequency of protein K-PTM types, and examines the relationship between protein similarity and differences in K-PTM-type frequency to investigate why the model can successfully predict this target.

The Coherence Response Index: predicted microRNA targets show no coherent regulation in chemically exposed mouse embryonic stem cells.

Toxicogenomic studies increasingly promote microRNA (miRNA) expression changes as chemical-toxicity biomarkers and infer their meaning from computationally predicted messenger RNA (mRNA) targets, rarely testing those predictions against matched mRNA data. We present the Coherence Response Index (CRI), an open, expressi...

Template-dependent conformational remodeling induced by matched mutation sets in an artificial metalloenzyme.

An ensemble-based model in which pre-existing conformational organization shapes how the protein responds to the matched mutations is supported and stability-engineering mutations should be evaluated in the context of the parent ensemble is argued.