protein structure

Frequency-Dependent Structural Responses of Amyloid-β Fibrils to Terahertz Pulses: A Nonequilibrium Molecular Dynamics Study

This study uses nonequilibrium molecular dynamics to show frequency-dependent structural changes in amyloid fibrils under terahertz pulses, identifying two electric-field thresholds for disruption.

RPFace: From biased structural benchmarks to generalizable RNA-protein interface prediction

RPFace predicts RNA-protein interfaces directly from sequence, outperforming existing methods on RNA interfaces and generalizing to in vivo data without pretraining.

Charting the Structure and Functional Landscape of the SF3B1 Intrinsically Disordered Region

This study characterizes the conformational dynamics and phosphorylation-dependent changes in the SF3B1 N-terminal domain using a combination of biophysical and computational methods.

FoldAbS: Repurposing the Protein Folding Model as a Foundation Encoder for Antibody Screening

FoldAbS repurposes protein folding models as foundation encoders to improve antibody screening by evaluating specificity, affinity, and developability in a unified framework.

bL9 prevents recoding in collided ribosomes

This study shows that bL9 prevents recoding events in collided ribosomes by stabilizing their interaction and reducing frameshifting and hopping.

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.

All-Atom Structure Tokenizer: AtomLM-9b for Biomolecular Structure Prediction

The paper introduces AtomLM-9b, a language model using an all-atom structure tokenizer to predict protein structures with performance comparable to AlphaFold 3.

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.

Disulfide Crosslink Density is a Key Determinant in the Formation, Dynamics, and Maturation of Cysteine-rich Designer Biomolecular Condensates.

This study identifies disulfide crosslink density as a critical factor in controlling the formation, fluidity, and maturation of cysteine-rich biomolecular condensates.

Representation-aware calibration enables statistically reliable protein structure search

Struct-Caliper improves protein structure search reliability by providing accurate p-values, increasing homolog recovery and reducing false discoveries compared to native E-values.

Direct NMR evidence for transient binding of the vesicular SNARE protein synaptobrevin-2/VAMP2 to the α-synuclein C-terminus

This study provides direct evidence of transient binding between α-synuclein C-terminus and synaptobrevin-2 using NMR and other biophysical methods, suggesting a role in neuronal exocytosis.

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.

AI-based structural modelling and pathogenic variant mapping across the human protein interactome

The paper uses AI to model 109,282 human protein interactions, maps pathogenic variants to these structures, and identifies interface mutations in disease contexts.

Res ipSAE adhuc loquuntur: What the directionality of predicted aligned error in cofolding models can tell us about scoring diverse molecular complexes

This paper introduces ipSAE, a directional scoring framework for assessing confidence in predicted biomolecular complexes, showing improved performance over existing methods in protein-ligand and protein-DNA interactions.

A cotranslational role for selenocysteine in productive protein folding

This study shows that selenocysteine (Sec) plays a role in protein folding during biosynthesis, not just in mature proteins, by demonstrating that its incorporation affects dimer formation in SELENOM.

Natural genetic diversity modulates structural stability changes caused by pathogenic variants in small proteins

The paper evaluates how natural genetic diversity affects the thermodynamic impact of pathogenic variants in small human proteins, showing significant background-dependent stability changes in most tested variants.

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.

Selective binders of a cotranslational folding intermediate

The paper identifies cyclic peptides that selectively bind to a cotranslational folding intermediate of β-galactosidase, revealing a druggable pocket formed during translation.

ToxINsight: An Integrated Web Platform for Sequence, Structure, and Ligand Binding Analysis of Snake Venom Toxins

ToxINsight provides a web platform for analyzing snake venom toxin sequences, structures, ligand interactions, and geographical distributions to aid in antivenom development.

Structure of influenza D virus NS1 reveals a novel Zn-binding site and ssRNA-binding activity

This study determines the structure of influenza D virus NS1, identifies a novel Zn-binding site and RNA-binding activity in its CTD, and shows their importance for viral replication.

Structure of Bacillus cereus ZmaM, a peptidase-ABC transporter that secretes and activates zwittermicin A

The paper structures ZmaM, a type II peptidase-ABC transporter in B. cereus, showing it activates and exports zwittermicin A by coordinating peptidase and transporter modules.

Computational Repurposing of FDA Approved Drugs Against Cyclin Dependent Kinase (CDK2)

The paper identifies FDA-approved drugs with potential binding activity against CDK2 using computational methods and selects Carteolol as a candidate.

Differentiable Spin-Center Diffusion Model Enables DEER-Guided Generative Pipeline of Weighted Protein Ensembles

This paper introduces a differentiable spin-center diffusion model to generate weighted protein ensembles from DEER spectroscopy data, enabling thermodynamic interpretation of conformational ensembles.

Laminin-Derived Peptides Bind Neuropilin-1 at the VEGF-A165 Binding Pocket

The paper investigates whether laminin-derived peptides bind to the VEGF-A165 binding pocket of NRP-1 using computational and experimental methods, finding that peptide 1 has the highest binding occupancy.

Improving Molecular Docking Pose Recovery through Targeted Side-Chain Monte Carlo Sampling of an Apo Structure

The paper improves molecular docking by using targeted side-chain Monte Carlo sampling of an apo structure, achieving better ligand pose recovery than apo or restrained MD approaches.

Structure-resolved fold annotation of the medicinal-leech salivary-EV cargo: a Ly-6/uPAR three-finger scaffold and a structurally dark fraction

The paper uses structure prediction to annotate the fold of uncharacterized proteins in medicinal leech salivary EVs, identifying one as a Ly-6/uPAR three-finger fold and leaving others unresolved.

EpiRank: partner-agnostic surface-patch retrieval for epitope prediction of protein binding interfaces

EpiRank evaluates epitope prediction by ranking surface patches on single-chain geometry, finding it correctly identifies real epitopes 64% of the time but with significant baseline overlap.

Structure of a secreted lancelet carotenoid cleavage dioxygenase (CCD), from an ancestral CCD clade

The paper presents the structure and functional properties of a BCOL protein from the lancelet Branchiostoma floridae, revealing structural and sequence differences from other CCDs.