protein folding

Phosphorus Limitation Differentially Affects Growth, Phosphate Consumption, and Carbon Allocation in Chlamydomonas reinhardtii Batch Cultures Under Photoautotrophic and Mixotrophic Conditions

Overall, it could be concluded that trophic conditions strongly affect phosphorus requirements, phosphate consumption, and carbon allocation, thereby shaping the adaptive response of C. reinhardtii to phosphorus limitation.

Graded degradation of nucleotide second-messenger signaling and selective retention of structural metalloproteins in the Kryptonia phylum

ProbJanusDDG: pretrained models and frozen ESM2 embeddings

Frozen full-length ESM2-650M embeddings and five pretrained ProbJanusDDG fold models used for protein-stability prediction with median ensemble predictions and protein-weighted empirical standard/adaptive CV+ intervals. Companion code: https://github.com/bardu98/ProbJanusDDG, commit 6cbf41c500a9108b6c3e065e370b8946bbd1...

AI-Guided De Novo Design Pipeline for Oral, Gut-Active Peptides That Stimulate GLP-1 Secretion and Promote Weight Loss in Diet-Induced Obese Rats

Glucagon-like peptide-1 (GLP-1) receptor agonists have transformed obesity treatment, yet gastrointestinal intolerance, high cost and weight regain after discontinuation highlight the need for complementary strategies. Stimulating endogenous GLP-1 via nutrient-sensing G protein-coupled receptors on enteroendocrine L...

yoonalimsuwan/REAL-FOLD-ONE: REAL FOLD ONE 17 Non PCF Fractal 22 Order Operator : SOC‑Controlled Universal Refinement , Predictor & High‑Throughput Mutation Scanning Suite And De Novo Protein Design , CRISPR-Cas Development (Design) And Chips Design (Classic , Quantum)

A unified physics‑based framework for macromolecular refinement , Predictor and mutational scanning. Built around a novel Self‑Organised Criticality (SOC) controller, it refines proteins, DNA, RNA, and their complexes using a fully differentiable energy function powered by OpenMM, then scales to thousands of in silico...

Flock: A Negative-Enriched Protein–Protein Interaction Dataset

Protein–protein interactions (PPIs) govern fundamental biological processes and are central to therapeutic discovery, yet computational prediction methods remain severely limited by a lack of high-quality negative data (non-interacting PPIs). Existing models are trained almost exclusively on positive interactions or ra...

An affibody in complex with a target protein: structure and coupled folding

Data and software for: Does AlphaFold 3 Replace Protein–Protein Docking? A Blind Benchmark Against Fast-Fourier-Transform Docking and an Appraisal of Interface Confidence

Complete data and software accompanying a benchmark of template-free AlphaFold 3 co-folding against blind, clustering-reranked fast-Fourier-transform docking on 20 protein–protein complexes from Docking Benchmark 5, spanning the rigid-body, medium and difficult tiers and three interface classes, together with negative...

yoonalimsuwan/EVOLUTION-ONE: EVOLUTION ONE 17 Non PCF Fractal 22 Order Operator : Standalone Multi‑Level Cancer Evolution Engine And High-Performance Epidemiological Forecasting , Viral Evolution Engine Latest And Ageing Latest

Evolution ONE is a standalone, vendor‑neutral platform that models cancer progression through the lens of Self‑Organised Criticality (SOC), duon biology, and physics‑based structural refinement. It ingests genomic mutation data (MAF, VCF) and outputs a complete oncological profile: the evolutionary regime of the tumour...

yoonalimsuwan/REAL-FOLD-ONE: REAL FOLD ONE 15 Full Version : SOC‑Controlled Universal Refinement , Predictor & High‑Throughput Mutation Scanning Suite And De Novo Protein Design , CRISPR-Cas Development (Design) And Chips Design (Classic , Quantum)

A unified physics‑based framework for macromolecular refinement , Predictor and mutational scanning. Built around a novel Self‑Organised Criticality (SOC) controller, it refines proteins, DNA, RNA, and their complexes using a fully differentiable energy function powered by OpenMM, then scales to thousands of in silico...

Supplementary Material for "Glycolysis-stratified coordination of fatty acid and glutamine metabolism in pancreatic ductal adenocarcinoma""

Update in this version: Supplementary materials were updated to align with the revised manuscript, including an updated graphical abstract and the addition of the High-versus-Low CPTAC-PDAC family-level permutation analysis (S8; Δr_meta = r_meta(High) − r_meta(Low; B=5000), with BH-FDR correction). Supplementary Materi...

A Transfer Learning Framework for Multilayer Networks via Model Averaging

Link prediction in multilayer networks is a key challenge in applications such as recommendation systems and protein-protein interaction prediction. While many techniques have been developed, most rely on assumptions about shared structures and require access to raw auxiliary data, limiting their practicality. To addre...