protein folding

Title: Phase Transition Modeling with Emergent Control

This paper presents a novel approach to modeling phase transitions, specifically focusing on the emergence of control within complex systems. We introduce a dynamic resonance field that evolves in response to the system's state, generating feedback loops that influence the transition process. This mechanism allows for...

Thermodynamic Profiling for Synonymous Variant Classification: When the Message Changes Without Changing the Protein

In synonymous variants, the signal of pathogenicity is detectable as a local, signed thermodynamic perturbation of nearest-neighbor nucleotide stacking — orthogonal to protein-level predictors — that a two-feature interpretable model reproduces at the level of a dedicated deep classifier, and whose clarity increases wi...

Molecular identification and statistical optimization of endo-α-amylase production by Bacillus licheniformis KeR9 isolated from potato roots for maltooligosaccharide synthesis

A starch-degrading bacterial strain (KeR9) isolated from potato root tissues was identified through whole-genome sequencing using average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) as Bacillus licheniformis . This strain with enzymatic production potential was then deposited in the Genbank project PRJNA1...

Title: Phase Transition Modeling with Emergent Control

This paper presents a novel approach to modeling phase transitions, specifically focusing on the emergence of control within complex systems. We introduce a dynamic resonance field that evolves in response to the system's state, generating feedback loops that influence the transition process. This mechanism allows for...

Thermodynamic Profiling for Synonymous Variant Classification: When the Message Changes Without Changing the Protein

In synonymous variants, the signal of pathogenicity is detectable as a local, signed thermodynamic perturbation of nearest-neighbor nucleotide stacking — orthogonal to protein-level predictors — that a two-feature interpretable model reproduces at the level of a dedicated deep classifier, and whose clarity increases wi...

Title: Dynamical Topology Optimization for Complexity

Dynamical Topology Optimization (DTO) provides a framework for optimizing complex network topologies by iteratively refining connections based on emergent properties. This paper introduces a novel algorithm, termed 'Adaptive Topology Evolution', which integrates reinforcement learning and graph theory to achieve automa...

The evolutionarily conserved C-terminal domain of a domesticated transposase-derived protein regulates its DNA integration ability

Programmable design of functional proteins from natural language

Pinal, a 16-billion-parameter foundation model that produces protein candidates from natural-language functional descriptions, supports natural language as a high-level interface for candidate generation in protein design, enabling programmable exploration with reduced reliance on manually specified structural or seque...

Development of a drug delivery vehicle protein exhibiting high binding affinity and low leakage of the anti-cancer drug SN-38.

It is demonstrated that simple amino acid substitutions in L-PGDS can optimize drug binding, improve solubility, and suppress drug release, thus providing a basis for affinity-driven design of protein-based DDSs.

Down-Regulated Fli1 in Scleroderma Myeloid Cells Contributes to Cardiac Fibrosis Via a Galectin-3/mTOR Dependent Pathway.

A myeloid Fli1-Gal-3-mTORC1 axis as a central pathway in SSc-associated cardiac fibrosis and a potential therapeutic target is identified, identifying a myeloid Fli1-Gal-3-mTORC1 axis as a central pathway in SSc-associated cardiac fibrosis and a potential therapeutic target.

Insights into the mechanism of enhanced tetramethylpyrazine production in dehulled adlay fermented by Bacillus subtilis BJ3-2.

Tetramethylpyrazine (TTMP) is a vital bioactive alkaloid and characteristic flavor compound in fermented foods. Our previous study found that fermentation of adlay by Bacillus subtilis BJ3-2 efficiently accumulates TTMP, whereas the underlying high-yield mechanism remains unclear. This study investigated the fermentati...

Hashi: Bridging Statistical Model Derived 1D Microstate Encodings and Protein 3D Structural Ensembles

Hashi is introduced, a pipeline to rapidly generate realistic structural ensembles from the outputs of the structure-based Wako- Saitô-Muñoz-Eaton (WSME) statistical mechanical model of protein folding, applicable to a variety of single-chain monomeric systems.