protein folding

Formation and Ecological Dynamics of Synthetic Biofilms Derived from Microbial Components of the Cladonia arbuscula Thallus

Synthetic multi-species consortia provide valuable insights into the ecological and structural dynamics of complex microbial biofilms. However, the specialized functional contributions of individual components under severe nutrient limitations remain poorly understood. This study investigated the population dynamics, m...

A curated benchmark for cofolding models on kinase conformational states

KinConfBench is introduced, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states.

Coupling intensified push–pull technology with insect frass biofertilization improves land productivity, protein yield and carbon stocks

We evaluated agricultural innovations such as push-pull (PP), vegetable-integrated push-pull (VIPP), and black soldier fly frass fertilizer (BSFFF) for their transformative potential in rural smallholder agriculture. Using 12 cropping systems comprising two crops (maize and cowpea), BSFFF and diversified systems (PP an...

YES1, a plasma-based biomarker for cavernous malformations.

A putative diagnostic biomarker for CCM, YES1, was demonstrated to be significantly elevated in the plasma of affected patients, with high correlative expression in the source tissue, which further support the development of CCM-related noninvasive biomarkers and may add insight into their pathogenesis.

NitroXAI: An Interpretable Deep Learning Framework for Human S-Nitrosylation Site Prediction

NitroXAI v0.1.1 is an interpretable framework for residue-level S-nitrosylation (SNO) site prediction. The release provides two frozen ensemble predictors for identifying candidate S-nitrosylated cysteineresidues from complete protein sequences: • SNO-CLIM: a lightweight CNN-BiLSTM baseline using handcrafted biochemica...

Engineered genomic attachment sites for site-specific recombinases enable high-efficiency integration in plants and human cells.

Here we developed a DNA-centric strategy for optimizing site-specific recombination by rationally engineering chimeric attachment sites. The high-activity att variants enhance Bxb1-mediated integration efficiency in human cells and plants. Among these att variants, the engineered attB(V111) site achieved 51.9% integrat...

NitroXAI: An Interpretable Deep Learning Framework for Human S-Nitrosylation Site Prediction

NitroXAI v0.1.1 is an interpretable framework for residue-level S-nitrosylation (SNO) site prediction. The release provides two frozen ensemble predictors for identifying candidate S-nitrosylated cysteineresidues from complete protein sequences: • SNO-CLIM: a lightweight CNN-BiLSTM baseline using handcrafted biochemica...

Decoding protein mutational fitness through evolutionary sequence intelligence: a large-scale ESM-2 benchmark across 217 DMS assays

Quantifying molecular specificity in excipient-driven antibody solubilization

It is shown that excipient-mediated solubilization of therapeutic antibodies is markedly molecularly specific, and the integration of high-throughput experimentation with molecular feature analysis offers a foundation for improving the understanding and prediction of antibody-specific formulation behavior.

FoldKit: A Python library for efficient storage and retrieval of co-folding predictions

FoldKit is introduced, a Python package for efficient storage and analysis of large-scale AF3 co-folding results that reduces storage requirements and facilitating programmatic access to relevant outputs, which facilitates large-scale computational studies of biomolecular interactions.

Dehydrocorydaline Accelerates Palatal Wound Healing in Mice Through Suppression of the p38 MAPK/CCL2 Axis and Macrophage Chemotaxis: A Preliminary Study

Investigating whether DHC accelerates palatal wound healing and to elucidate the role of the p38 mitogen-activated protein kinase (MAPK)/CCL2 signaling axis in DHC-mediated regulation of macrophage chemotaxis demonstrated that DHC accelerated palatal wound healing 1.6-fold in mice.

5 A multivariate plasma biomarker model enabling safe exclusion of glioblastoma

A plasma-based multivariate biomarker model enables accurate, safe exclusion of glioblastoma and supports diagnostic triage alongside neuro-imaging and maintains an extremely high NPV (>0.999), consistent with its intended role as a high-sensitivity exclusion tool rather than a confirmatory test.