protein design

Engineering Nanobody Conformational Switches

This paper engineers conformational switches using nanobodies that fold upon ligand binding, enabling customizable receptors and sensors for biomarkers and drugs.

StableProt: Structure-Aware Deep Learning for Protein Thermostability (Tm) and Environmental Adaptation (OGT) Prediction

StableProt predicts protein thermostability and organismal optimal growth temperature using a structure-aware deep learning framework, achieving high accuracy and robustness across temperature regimes.

pLM-bVAE: protein language model-enhanced binary representation improves quantum annealing-based protein sequence design

This paper introduces pLM-bVAE, a binary variational autoencoder enhanced with protein language model representations, showing improved sequence reconstruction and design performance in quantum annealing-based protein sequence design.

PartiDesign: A structure-sequence co-design paradigm for practical all-to-all biomolecules design

PartiDesign is a structure-sequence co-design model that generates molecular structures and sequences for proteins, nucleic acids, and small molecules, achieving high design throughput across benchmarks.

AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces

This study evaluates AlphaFold 3's accuracy and reliability in predicting RNA structures and protein-RNA interfaces, finding that confidence scores do not always correlate with correct predictions.

Functional analysis of small-molecule and protein binding domains using monomeric streptavidin-based two-component biosensors

The paper develops a biosensor platform using monomeric streptavidin to evaluate binding domains for small molecules and proteins, demonstrating ligand-dependent activation with biotinylated targets.

Mapping and Probing the Substrate Scope of a Ketoamide-Forming Splicease by Computational Design

The paper uses computational methods to design and evaluate splicease variants for generating diverse ketoamide substrates, finding that top-scoring peptides are spliced more efficiently than single-point mutants.

Filament assembly confers the mechanical resilience of the IFI16 restrictosome

This study shows that IFI16 filament assembly provides mechanical stability to condensates by compacting DNA into ultra-stable tangles, contrasting with the sensitivity of HIN200-dsDNA complexes.

Target Specific Conformational Flexibility and Electrostatic Complementarity Modulate LTNF10 Peptide Binding to Phospholipase A2 Variants from Snake Venoms

This study investigates how charge and conformational changes in a peptide affect its binding to different snake venom PLA2 variants, revealing structural and electrostatic factors influencing affinity.

Conformation governs cellular behaviors of LRRK2 Parkinson's disease variants

This study identifies 'unlatching' as a common mechanism for Parkinson's disease-associated LRRK2 variants, showing increased membrane localization and decreased S935 phosphorylation.

Machine learning guided design of strong transcriptional activation domains

The paper designs functional transcriptional activation domains using machine learning and experimental validation, finding that over 90% of predicted sequences work in yeast.

De novo design of mini-proteins as specific binders to PACAP-38, a key mediator of migraine

This study designs mini-proteins that bind PACAP-38 with high affinity, showing improved potency and stability compared to earlier versions.