protein folding

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.

In silico evaluation of deleterious nsSNPs in SOD1 and TARDBP genes associated with amyotrophic lateral sclerosis

Network and pathway analyses highlighted SOD1 and TARDBP as key nodes in ALS-related mechanisms, such as oxidative stress, RNA metabolism, proteostasis, and mitochondrial impairment, and network-based functions were combined.

Functional Identification of Minimal Promoter Region of Elongation of Very Long Chain Fatty Acids 2 (ELOVL2) Gene in Chicken Hepatocytes

It can be concluded that both the promoter fragments of ELOVL2 are capable of regulating gene expression even in a cell culture system with the larger fragment being more effective.

A composite model incorporating systemic inflammatory burden and GRACE score for enhanced identification of elevated myocardial stress in acute myocardial infarction: an exploratory analysis

In this exploratory analysis, SIBS is associated with clinical severity and myocardial stress in AMI patients and a composite model combining SIBS, GRACE score, and hs-CRP improves identification of elevated myocardial stress compared with single biomarkers in this exploratory analysis.

SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding

This work introduces a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.

Functional Analysis of the Heat-Tolerance Candidate Gene BcNCED3 in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis)

It is demonstrated that BcNCED3 positively regulates thermotolerance in non-heading Chinese cabbage and provide a genetic resource for heat-tolerance breeding.