protein folding

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...

Genome-wide identification and characterization of the galactinol synthase (GmGolS) gene family and its expression under drought, heat, and combined stress in soybean

Abstract Galactinol synthase (GolS) catalyzes the first committed step in raffinose family oligosaccharide (RFO) biosynthesis and is implicated in plant adaptation to abiotic stress. Although GolS gene families have been characterized in several plant species, a comprehensive genome-wide analysis in soybean has been la...

Temporally Validated Models for Target “Tclin-likeness”

Abstract Identifying which human proteins are likely to become validated drug targets remains a challenge in drug discovery. We build on the “Tclin” concept, which encompasses proteins for which at least one approved drug exerts its mode of action (MoA); these comprise only ∼3% of the human proteome. We developed disea...

The Topological Mechanics of Protein Recognition

This deposit contains the complete monograph, formal mathematical proofs, software implementations, and supplementary computational assets introducing The Topological Mechanics of Protein Recognition, an exact algebraic-topological and geometric framework for de novo therapeutic protein design. Heretofore, a central an...