protein structure

SAR11 Genome Atlas: a genome and gene catalog for functional profiling of the most abundant bacterial clade in the ocean

The paper introduces the SAR11 Genome Atlas, a resource integrating SAR11 genomes and functional data to support ecological and genomic analysis of oceanic bacteria.

In situ loading of biologics on and tissue redirection of circulating extracellular vesicles with an anchoring nanobody

This paper demonstrates that NEV3, an EV-anchoring nanobody, enables in situ loading of proteins onto circulating extracellular vesicles and redirects them to specific tissues in vivo.

De novo Protein Generating Model via Structure-Aware Graph Neural Networks

This paper introduces a protein conformation prediction model optimized for structural accuracy using a structure-aware GNN, achieving results comparable to sequence-focused methods without sequence recovery supervision.

Structural Basis for Dual Peptidoglycan Hydrolysis by an E. faecium Minhovirus Tail Spike Lysin

The paper characterizes ORF11, a tail-spike lysin from E. faecium Minhovirus, revealing its dual peptidoglycan hydrolysis activity through structural and biochemical analysis.

Neopep: Reinforcement Learning From Machine-Learned Force Field Energy for Non-Canonical Peptide Structure Prediction

Neopep uses reinforcement learning with machine-learned force field energy to predict structures of non-canonical amino acid-containing peptides, achieving lower RMSD than existing methods.

Site Specific Hydration Contributes to the Thermal Stability of Proteins and Protein-Complexes

This study investigates how site-specific hydration affects the thermal stability of proteins and protein complexes using D2O and experimental methods, revealing that stabilization depends on both hydration extent and water interaction sites.

Discrete-time quantum walks reveal critical residues involved in long-range interactions in proteins

The paper uses discrete-time quantum walks to predict critical residues in proteins involved in long-range interactions, validated experimentally on AsLOV2.

Predicting conformational changes induced by biomolecular interactions

This paper introduces K-Fold, a method that improves prediction of conformational changes in protein complexes by modeling structural transitions from unbound to bound states.

Photoactivatable Rac1: a photosensor tilt by time-resolved crystallography and a partially open switch I when GDP-bound

This paper uses time-resolved crystallography to visualize how light activates Rac1 by tilting the LOV2 domain and partially opening switch I when GDP-bound.

Discovering and designing multistate protein assemblies

This paper designs protein assemblies that switch between structural states using engineered interfaces, demonstrating temperature-responsive transitions from capsids to 2D arrays.

Structural conservation and expanded functionality of hyper-stable human serum albumin variants

This study validates engineered hyper-stable human serum albumin variants for their structural integrity and functional adaptability in biotechnological applications.

De novo design of light-controlled conformational protein switches

This paper computationally designs light-responsive proteins that undergo conformational changes upon light activation, enabling precise control of biological functions.

An Interactive Bidirectional De Novo Protein Design System

This paper introduces an interactive server that combines a structure-aware GNN and ESMFold for bidirectional protein design, enabling users to analyze and validate design hypotheses without software installation.

From {triangleup}{triangleup}G Prediction to Mutation Prioritization with Conformal Prediction

The paper introduces ProbJanusDDG to prioritize mutations for experimental follow-up by using conformal prediction intervals to assess uncertainty in predicted stability changes.

G4 RNA inhibits PRC2 by sequestering two disordered loops required for nucleosome binding

This study shows G4 RNA inhibits PRC2 by binding to disordered loops in EZH2, preventing nucleosome interaction and modulated by SAM and peptides.

BzAM terpolymer series with a step-wise systematic change in hydrophobicity, provides a nuanced platform for functional analysis of GPCRs in native-like nanodiscs

This paper introduces a series of BzAM terpolymers with varying hydrophobicity to solubilize GPCRs in nanodiscs, showing that solubilization efficiency and functional integrity are preserved.

Tumor SETDB1 expression predicts worse overall survival for bladder cancer patients

This study shows that high SETDB1 protein expression in bladder cancer is linked to shorter overall survival and specific tumor features.

Human prion proteins and mutants through the lens of systems biology

The paper uses network analysis, MD simulations, and experiments to identify critical residues in human PrP that affect structural stability and misfolding.

Integrative Biophysical Illumination of the 3D GPCRome Dynamics

The paper develops GPCRmd-NMR, an integrative platform combining MD simulations and NMR spectroscopy to analyze GPCR dynamics at unprecedented scale.

High-Throughput FRET Affinity Screening Technique (HTFAST) For Cell-Free Expressed Binding Protein Characterization

HTFAST enables high-throughput, quantitative affinity measurement of cell-free expressed binders using FRET, validated with nanobodies and SARS-CoV-2 sdAbs.

Structural and Energetic Determinants of Monobody Recognition of Oncogenic KRAS Variants

This study identifies structural and energetic determinants of monobody 12D4 recognition of KRAS variants using simulations and redesign, revealing key interactions and mutations for improved selectivity.

NMR-measured Per-residue Electrostatic Potentials Reveal the Importance of Arginine-Lysine Balance on the Conformational Ensemble of Disordered Histone H3 Tails in Nucleosome Core Particles

The paper measures electrostatic potentials of histone H3 tails using NMR and simulations to show how arginine-lysine balance affects their conformational behavior in nucleosome core particles.

Polymorphic Structures of an Artificial Nucleocapsid Evolved from a Circularly Permuted Bacterial Protein Cage

This study evolves an artificial nucleocapsid from a circularly permuted bacterial protein cage, revealing heterogeneous cage architectures with distinct subunit arrangements and conformations.

A structural screen for candidate polyphosphate binding surfaces in human membrane associated proteins

The paper develops a computational workflow to identify candidate polyphosphate binding surfaces in human membrane-associated proteins using structural and sequence-based approaches.

Rapid and Reliable Structural Modeling of Adaptive Immune Receptors Using an Optimized AlphaFold3 workflow

This paper optimizes AlphaFold3 for rapid and reliable structural modeling of antibodies and T-cell receptors, achieving 45-fold faster MSA phase and 3.6-fold faster inference.

Can Folding Models Tell Binders from Bluffers? Evidence from POISK: The Patent-Derived Antibody Dataset

The paper benchmarks structure prediction models on a new antibody dataset to assess their ability to distinguish binders from decoys, finding moderate success but limitations in epitope localization.

Design of full-length agonist and antagonist antibodies for hard targets

This paper designs full-length agonist and antagonist antibodies for hard targets using a computational pipeline, achieving nanomolar affinities and functional activity.

Integrated Framework for Probing Multimodal Protein Foundation Models with Structure-Functional Interpretability Analysis in Detection of Allosteric Binding Sites

The paper evaluates multimodal protein foundation models for allosteric binding site detection, finding that dataset properties, not model complexity, primarily determine performance.

SAbDab2: The structural antibody database in the age of machine learning

SAbDab2 provides updated antibody structures with machine learning-ready data and standardized splits for research.

Primary Human Macrophages Exhibit Functional CYP3A4 Activity with Marked Expression-Function Discordance and Cocaine-Induced Catalytic Activation

This study shows human macrophages have functional CYP3A4 activity, with expression and function discordance, and cocaine increases CYP3A4 activity across donors.