protein folding

Scoring close linker analogues in PROTAC ternary complexes: A matched-pose study of VHL-recruiting SHP2 degraders

Linker optimisation in targeted protein degradation remains largely empirical, and a computational method able to rank close analogues before synthesis would be valuable. Whether current methods can do so has not been tested against the smallest chemical difference that changes potency. Here two VHL-recruiting SHP2 deg...

Semi-synthesis of indole-fused taraxerone derivatives from Rhizophora stylosa Griff.: anti-bacterial study and docking insights

A series of novel semisynthetic indole-fused taraxerone derivatives (2a–2f) were synthesised from taraxerone isolated from Rhizophora stylosa Griff. and characterised by 1H NMR,13C NMR, and HRMS analyses. Incorporation of the pharmacologically important indole moiety was aimed at enhancing protein-ligand interactions a...

War-related proxy-reported distress behaviors are associated with childhood anemia: cross-sectional evidence consistent with inflammatory pathways in conflict-affected Yemen

Children in conflict zones endure chronic psychosocial stress with unclear biological consequences. We examined whether war-related caregiver-reported distress behaviors are associated with childhood anemia and whether systemic inflammation is consistent with a proposed statistical mediating pathway in Yemen, using a c...

NEUROCODEX: DECODING THE ALGORITHMIC ARCHITECTURE OF THE LIVING BRAIN HOW BIOLOGY INVENTED THE ALGORITHMS THAT RUN THE UNIVERSE

NEUROCODEX presents a revolutionary paradigm shift in neuroscience: the brain is not a computer, but rather the original algorithmic architect from which all artificial intelligence is merely a primitive derivation. This treatise demonstrates how biological systems achieve extraordinary energy efficiency (20 watts vers...

Litopenaeus vannamei heat shock protein 10 is a novel immune regulator that enhances shrimp defense against Ecytonucleospora hepatopenaei infection through LvSPL3-mediated prophenoloxidase activation.

Small heat shock proteins (sHSPs) are ATP-independent chaperones synthesized by cells in response to various stresses, including pathogen infection, to maintain cellular and protein homeostasis. However, their roles in shrimp innate immunity remain largely unknown. Here, we demonstrate that LvHSP10 is a key immune regu...

Rab Interactions identified by DEEPN.

Rab GTPase Y2H Interactome — Verified Hit DatasetThis dataset contains the curated set of protein-protein interactions identified in a yeast two-hybrid (Y2H) screen against 36 human Rab GTPases, each tested in both nucleotide-locked conformations: GTP-bound (constitutively active, Q→L mutant) and GDP-bound (dominant-ne...

Disease-first public-data integration with local virtual knockout prioritizes shared proteins linking osteoarthritis and osteoporosis

Osteoarthritis and osteoporosis frequently coexist in older adults, but shared molecular programs remain unclear. We developed a disease-first multilayer public-data integration framework to identify shared protein candidates while preserving disease-specific structure before cross-disease comparison. Public bulk trans...

Functional Stability Theory III: Biological Stability and Nash Frustration

A conjectural framework for biological organization spanning molecular to ecosystem scales, organized around thermodynamic game theory and the Maximum Entropy Production Principle (MEPP). The paper examines whether many biological stability problems can be modeled as dissipative structures whose attractors admit Nash-s...

Scalable saturation mutagenesis reveals gene regulatory architecture and rare variant effects

Long-context sequence-to-function models enable nucleotide-resolution prediction of regulatory variant effects, motivating comprehensive mutational interrogation across broad genomic contexts. Yet conventional in silico saturation mutagenesis (ISM) scores mutations one at a time, requiring millions of model evaluations...

Influence of Actinomucor elegans Fermentation on Protein Degradation, Flavor Development, and Nutritional Quality of Tofu

Clinical features associated with macrophage activation syndrome in juvenile dermatomyositis: implications for early recognition

This study aimed to characterize the clinical and laboratory features associated with juvenile dermatomyositis-associated macrophage activation syndrome and to identify warning features that may facilitate recognition of concurrent MAS at JDM presentation. The distribution and potential discriminatory contribution of m...

Responses of the model crop plant Ocimum basilicum L. grown hydroponically to combined hypoxia and salinity

Basil ( Ocimum basilicum L., cv Genovese) cultivated under hydroponic conditions was subjected to salinity, hypoxia, and combined stress for varying lengths of time to assess growth, metabolic, and antioxidant responses. Analyses demonstrated that stress type was the primary factor influencing plant responses, with tre...