protein folding

esm2-layer-invariance: conditional layer invariance in protein language models (BIOINF-2026-2348 revision)

Complete analysis pipeline and per-dataset results for the revised version of BIOINF-2026-2348. Includes: (1) unified per-layer probing of ESM-2 650M and SaProt_650M_AF2 on all 63 ProteinGym substitution datasets under three feature arms (masked wild-type, unmasked wild-type, mutant) and four train-test splits (random,...

esm2-layer-invariance: conditional layer invariance in protein language models (BIOINF-2026-2348 revision)

Complete analysis pipeline and per-dataset results for the revised version of BIOINF-2026-2348. Includes: (1) unified per-layer probing of ESM-2 650M and SaProt_650M_AF2 on all 63 ProteinGym substitution datasets under three feature arms (masked wild-type, unmasked wild-type, mutant) and four train-test splits (random,...

A homozygous hypomorphic FBN1 splice region variant in domestic cats with Marfan syndrome

Marfan syndrome (MFS) is an autosomal dominant connective tissue disease caused by variants in the fibrillin 1 ( FBN1 ) gene. While common in humans, spontaneous animal models are rarely reported. We present the first phenotypic and molecular characterization of MFS in domestic cats. A pair of random-bred littermates e...

Tardigrades have a complete condensin II: two divergent CAP-H2 kleisins in three eutardigrade genomes

Condensin II shapes interphase genome architecture: species that lack it tend to fold their chromosomes in a Rabl-like, type-I configuration, while species that have it form chromosome territories (type II). In the study that established this, the tardigrade Hypsibius dujardini (now H. exemplaris) was the only species...

Comparative Machine Learning and Graph Neural Network Approaches for Blood-Brain Barrier Permeability Prediction

Versioned research release of the BBB permeability prediction project. This release preserves the complete source code, experimental results, documentation, figures, and reproducibility materials for the project. Contents: Phase 3: 5-fold scaffold CV classical ML (RF AUROC 0.921+/-0.024) Phase 4: Chemprop GNN ensemble...

Comparative Machine Learning and Graph Neural Network Approaches for Blood-Brain Barrier Permeability Prediction

Versioned research release of the BBB permeability prediction project. This release preserves the complete source code, experimental results, documentation, figures, and reproducibility materials for the project. Contents: Phase 3: 5-fold scaffold CV classical ML (RF AUROC 0.921+/-0.024) Phase 4: Chemprop GNN ensemble...

AI-Model Integration for Predictive and Data-Driven Plant Systems Biology in Climate-Smart Agriculture

The integration of artificial intelligence (AI) in plant system biology enables the understanding of plant organization, revealing complex relations at the biological level. Plant systems biology aims at resolving the complex networks that define growth, development, stress responses, and metabolism by reframing inform...

pH cycling-induced structural remodeling of walnut protein-whey protein isolate complex: Trade-off between digestibility and bioactivity.

The bioactivity of plant proteins is often limited by the compact and aggregated structures. In this study, the walnut protein-whey protein isolate (WP-WPIp) complex was constructed via pH cycling. This treatment appeared to induce conformational changes characterized by a disordering of secondary structures and a disr...

Anagrelide remodels the PDE3A-SLFN12 interactome to associate with translation initiation machinery in cancer cell lines.

In this proposed model, anagrelide remodels the interactome of the PDE3A-SLFN12 complex, which relocalizes and accumulates near the mRNA entry channel of the 43S pre-initiation complex, which provides important mechanistic context for how PDE3A modulators act within the cell.

Computational Modeling and MM-PBSA-Based Molecular Dynamics Investigation of Unexplored tRNA Isoleucine Lysidine Synthetase from Mycobacterium tuberculosis with Hyperbranched Amoxicilloyl-Poly-L-Lysine

Preliminary computational evidence supporting MtTilS as target and APL-3 as putative inhibitor candidate necessitating further experimental validation is provided, with preliminary computational evidence supporting MtTilS as target and APL-3 as putative inhibitor candidate necessitating further experimental validation.

Decoding AlphaFold Through the Hamouda Informational Gravity Model (HIGM): Protein Folding as an Emergent Informational Optimization Process

Conformational Landscape of a Marginally Disordered Protein HYPK and its Charge-Variant Mutant in the Context of Folded Domains

All-atom molecular dynamics simulations are used to understand the sequence-specific and structural origin of marginality in HYPK by investigating the conformation landscape of both the wild-type and a charge-variant mutant of HYPK, with and without fluorescent proteins attached at the N- and C- termini.