protein folding

Targeted finetuning enables co-folding models to learn ligand-induced protein conformational states

Advances in protein structure prediction have enabled all-atom protein-ligand co-folding models that predict bound conformations directly from sequence and small-molecule structure. However, these models often fail to generalize to novel binding sites or alternative protein conformational states, limiting their utility...

Combining CHARMM36m with OPC water improves accuracy

Atomistic simulations of intrinsically disordered proteins (IDPs) are notoriously sensitive to force field inaccuracies, either regarding the protein or the water model, yielding inaccurate observables such as compactness, secondary structure propensities, or kinetics. The currently most widely used IDP force fields ar...

There Is No Pathlessness: An Investigation of Freedom as the First Cause — Architecture of Freedom Intelligence as a Useful Theory of Reality, Navigation, Design, Physics, and Path Availability

I propose that freedom is the true cause of reality because freedom means path availability, and there is no possibility of pathlessness. Everything that exists navigates: water down a slope, photons through a slit, ions across a membrane, a child across a room, a household across a budget. Intelligence is the capacity...

Golden Ratio Encoded in Icosahedral Capsid Geometry via Caspar-Klug T-Numbers — E8 Intelligence Research

FINDING: Icosahedral viral capsid geometry is governed by the Caspar-Klug T-number, which quantizes the surface lattice into pentamer/hexamer clusters, directly encoding the golden ratio in its pentagonal substructure. | MATH: T = h² + hk + k² (h,k ≥ 0 integers); capsid has 60T protein subunits; 12 pentamers + 10(T−1)...

Protein Structure Prediction Using AlphaFold: A Deep Learning Approach.

Abstract: Predicting the three-dimensional structure of a protein directly from its amino-acid sequence has remained one of the most persistent open problems in computational biology, commonly referred to as the protein folding problem. For decades, structural information was obtainable only through slow, expensive, an...

A Constraint-Space Perspective on Coordinated Gene Expression in a Minimal Cell

This is a Perspective article. Two recent Cell studies (Dobbs et al., 2026; Jensen et al., 2026) used in-cell cryo-electron tomography and visual proteomics in Mycoplasma pneumoniae to resolve structural coordination among transcription, translation, membrane translocation, and extracellular folding.We offer a theoreti...

Microbial cells reprogram energy and protein metabolism in response to plastic exposure

Predicting Transmembrane Protein Topology from 3D Structure

A novel approach to infer protein topology using the state-of-the-art graph neural network (GNN), SchNet, trained on the same dataset used to develop the recent DeepTMHMM model with 5-fold cross-validation.

Pathways of early evolution from the perspectives of a riboreplisome -- the ultimate RNA machine of life

It is proposed that early replication and protein biosynthesis were inseparable functions performed by a single ancient RNA molecule: the riboreplisome, and this hypothesis addresses fundamental challenges facing RNA world, protein world, and RNA-protein co-evolution theories.

Mendelian Randomization and Bioinformatics Identify IFI27 as a Candidate Biomarker for Recurrent Pregnancy Loss in Systemic Lupus Erythematosus.

These findings identify IFI27 as a candidate biomarker shared by SLE and RPL; however, prospective clinical and experimental studies are required to validate its biological and clinical significance.

Quantum Approximate Optimisation Algorithm for Protein Sidechain Packing

A constraint-preserving ansatz is introduced, pairing a W-state initialisation with a cyclic XY ring mixer, that enforces one-hot rotamer validity without penalty terms while keeping two-qubit gate scaling linear in the rotamer count.

Collagen targeting IL-12 combined with doxorubicin enhances the anti-tumor effect against osteosarcoma.

It is demonstrated that CBD-IL-12 exhibited 4-fold enhanced tumor accumulation compared to unmodified IL-12 and increased cytotoxic T cell infiltration by 2.2-fold within the immune-cold microenvironment in a mouse model of OS.