Protein Structure and Dynamics

In Silico Structure-Based Interactomic Analysis of the Scaffolding Protein DCAF7

The paper identifies a conserved helical motif in DCAF7 partners using structural and computational methods, revealing its role in scaffolding and linking to neurodevelopmental disorders.

Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling

This paper introduces CRIM, a scoring function combining cryo-EM and IM-MS data to improve monomeric protein structure prediction, showing reduced RMSD and increased TM-score on both simulated and experimental datasets.

pH Induced Changes in Protein Structure and Hydration

This study investigates pH-induced structural changes in Hen Egg-White Lysozyme using simulations and experiments, revealing how titratable residues influence conformational fluctuations and hydration behavior across pH ranges.

Benchmarking Boltz-2 for Screening of Therapeutic Antibody-Antigen Interactions

The paper benchmarks Boltz-2 for screening therapeutic antibody-antigen interactions, finding weak but above-chance discrimination and limited benefit from extensive sampling.

Highly Accurate Estimation of the Fold Accuracy of Protein Structural Models

This paper introduces DeepUMQA-Global, a deep learning framework for estimating protein structure model accuracy, which outperforms existing methods in correlation metrics and consensus rankings.

Bayesian-Steered Structure Prediction of Mechanical Biomolecules Using Twisted Diffusion

This paper introduces a Bayesian-steered diffusion method for predicting alternative conformations of mechanical biomolecules, demonstrating its ability to reproduce experimentally validated states of various proteins and DNA.

Redesign selective protein binders using contrastive decoding

RedNet improves protein binder design by incorporating side-chain information and contrastive decoding to enhance binding affinity, folding stability, and selectivity.

Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling

This paper introduces OPES multithermal sampling to efficiently explore rare conformations in intrinsically disordered proteins, revealing transient tertiary structures in ACTR.

Large-scale discovery, analysis, and design of protein energy landscapes

The paper measures conformational fluctuations of protein domains using hydrogen-deuterium exchange mass spectrometry and uses computational modeling to design mutations that stabilize low-stability segments.

Unified sampling framework and experimental benchmarking of sequence- and structure-based protein models

The paper benchmarks sequence- and structure-based protein models using a unified framework, showing structure-based models outperform others in generating functional variants.

Statistical thermodynamics based design principles into the temperature induced fold switching of a metamorphic protein

This study uses thermodynamic analysis to uncover the molecular driving forces behind temperature-induced fold-switching in a designed metamorphic protein, providing a statistical thermodynamic framework for future protein engineering.

High-Speed AFM Reveals Ligand-Dependent Supramolecular Switching of Human Phosphofructokinase-1

This study uses HS-AFM and simulations to show ligand-dependent assembly switching of human PFKL, revealing structural changes in response to ATP and F6P.

AI-derived Protein Structures Validation: AlphaFold2 Models in the Twilight Zone

The paper validates AlphaFold2-generated protein structures by aligning them with structurally similar proteins, showing success for challenging cases like ABHD16A.

Leveraging neural networks to correct FoldX free energy estimates

This paper trains a neural network to correct FoldX's free energy predictions for protein folding and binding, significantly improving accuracy for single and double mutations and epistasis.

ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications

ProteinFlux predicts protein conformational dynamics influenced by post-translational modifications using a generative framework, outperforming traditional methods in speed and accuracy.

Conformational Diversity and Substrate Specificity are Decoupled in Ancestral and Extant Glucokinases

This study shows that substrate specificity in glucokinases is not linked to conformational diversity, as similar specificity ratios are observed across ancestral and extant forms with varying structural features.

Hero11 Unlocks TDP-43 Condensate Fluidity via Targeting Inter-Helical Interactions

This study shows Hero11 disrupts TDP-43 condensate structure by targeting helix-helix interactions, altering condensate fluidity and dynamics.

Reverse-engineering amyloid strains with generative protein design

This study uses generative protein design to explore how sequences encode amyloid fibril structures, showing a continuous compatibility between sequences and a common amyloid fold.

The impact of N-terminal dimerization on formin homology 1 (FH1) domain polymer dynamics and actin assembly

This paper develops a computational model of formin FH1 domain dynamics to study how N-terminal dimerization affects actin polymerization rates and cytoskeletal assembly.

LIVIA: a browser-based tool for assessing and visualizing predicted protein interactions

LIVIA is a browser-based tool that assesses and visualizes predicted protein interactions by computing confidence metrics and providing 3D visualization options.

A structural grammar of truncation across the human homodimer landscape

The paper systematically analyzes the structural impact of proteolytic truncation on human homodimers, identifying two rules governing interface preservation and emergence.

Know Your Alphabet: Conformational Noise, Latent-Space Encodings, and the Future of Structural Phylogenetics

The paper introduces a metric to quantify conformational noise in structural alphabets and shows its impact on phylogenetic inference using NMR ensembles and molecular dynamics simulations.

Structural bias in machine learning-guided peptide design

The paper audits structural biases in ML models for antimicrobial peptide design and finds that sequential training data lead to biased predictions due to uneven fold representation.

Simple baselines rival protein language models in dense combinatorial protein landscapes

This study compares protein language models (pLMs) with simple baselines in combinatorial protein design, finding no consistent advantage for pLMs in predicting or generating superior variants.

Local aromatic interactions define temperature sensitivity of phase separation in an intrinsically disordered protein.

The paper investigates how temperature sensitivity in phase separation of an intrinsically disordered protein is encoded by local aromatic interactions, showing that tyrosine residues mediate both structural stability and phase behavior.

The turn less taken: Investigating patterns in β-turn dynamics using large-scale molecular dynamics data

This study analyzes β-turn dynamics using molecular dynamics data to identify six types, including a hybrid I/I' cluster, and shows sequence and structural factors influence their conformational behavior.

Allosteric Protein Chemical Shift Perturbations are Ubiquitous

The paper analyzes NMR chemical shift perturbations in protein complexes to show that structural plasticity is widespread, with 74% of significant CSPs occurring non-locally to the binding site.

Assessing State-Specific Accuracy of Cofolding Models for Kinases and GPCRs

The paper evaluates cofolding models for kinases and GPCRs, finding that ligand accuracy often decouples from overall conformational state recovery, with implications for drug design.

Evolution of Protein Regulation in the Vertebrate Glucose Sensor

This paper reconstructs extinct glucokinase (GCK) and glucokinase regulatory protein (GKRP) to study the evolutionary origins of protein regulation in vertebrate glucose homeostasis.

Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways

This paper introduces a distance-restraint-guided diffusion model to sample protein conformational changes and ligand dissociation pathways, achieving uniform coverage and high structural quality.