Protein Structure and Dynamics

Generalizing Protein Fitness Prediction Across Distribution Shifts via Structural and Co-evolutionary Priors

This paper develops a framework for protein fitness prediction that improves generalization across distribution shifts by integrating structural and co-evolutionary information.

Myristoylation licenses disordered viral VP4 protein to anchor to and perforate the membrane through phase separation

This study shows that myristoylation of VP4 enables membrane anchoring, phase separation, and pore formation in enteroviruses through multiple functional roles.

Substrate accessibility of bovine milk proteins to a Pseudomonas metalloprotease reveals why caseins are more readily hydrolysed than whey proteins

The paper shows that caseins are more hydrolyzed than whey proteins by a metalloprotease due to differences in substrate accessibility across contiguous regions, not just single residues.

Toward a Transferable Representation of Protein Dynamics for Functional Prediction and Mechanistic Discovery

This paper introduces TIDGN, a deep learning method to encode protein dynamics into a transferable latent representation, achieving high AUROC in function prediction across different proteins.

Complex folding kinetics of multi-domain proteins disentangled with periodic forces by magnetic tweezers

The paper uses magnetic tweezers with periodic forces to study multi-domain protein folding kinetics, showing how periodic forces can enhance intermediate states and enable quasi-equilibrium analysis.

Characterization of cross-family conserved fragments

The paper characterizes cross-family conserved fragments, showing their structural and biophysical properties and their role in folding and stability.

RGI-Toolkit: Differentiable Restraints for Controllable Biomolecular Structure Prediction

RGI-Toolkit enables controllable biomolecular structure prediction by integrating experimental restraints into diffusion models without retraining.

Agentic campaign control for high-throughput de novo binder design

This paper introduces T-REX, an agentic framework for protein binder design that adaptively allocates compute resources across methods, achieving higher throughput of structurally distinct hits than baselines.

CropStabDB: a protein stability resource and Engineering Atlas of orthologue-supported substitutions for 30 plant proteomes

CropStabDB provides a resource of protein stability scores and substitutions across 30 plant proteomes, identifying residue changes that improve thermostability.

Quasi-continuous cotranslational compaction and folding of a multidomain protein

This study uses Force Profile Analysis to examine the cotranslational folding of Firefly luciferase, revealing a complex, quasi-continuous folding process with multiple intermediate steps.

PRIZM: Combining Low-N Data and Zero-shot Models to Design Enhanced Protein Variants

PRIZM uses low-N data and zero-shot models to rank protein variants, improving design efficiency with minimal experimental data.

How a highly acidic SH3 domain binds to its intrinsically disordered partner through the formation of an encounter complex intermediate

The paper investigates how the highly acidic SH3 domain binds to an intrinsically disordered partner through an encounter complex intermediate, revealing the role of long-range electrostatic interactions.

Ref(2)P/p62 protein pleomorphism confers tissue-specific function

One Drosophila Ref(2)P polypeptide takes different structures in midgut and muscle, driving autophagy or mitochondria-associated degradation; deleting disordered region IDR2 switches muscle Ref(2)P to midgut state.

trFlow: ultrafast all-atom protein conformational ensemble generation via conditional flow matching

trFlow generates all-atom protein conformations faster and more accurately than existing methods by using flow matching with three key innovations.

Generating Structural Ensembles of Disordered Proteins with Diffusion Models

The paper introduces Zephyr, a diffusion model for generating structural ensembles of disordered proteins, achieving high accuracy and faster sampling than molecular dynamics simulations.

GalaxyMemMD: an end-to-end Galaxy toolset for reproducible membrane embedding, molecular dynamics simulation, and analysis of membrane proteins

GalaxyMemMD provides a reproducible, high-throughput pipeline for membrane protein simulation and analysis, integrating embedding, MD simulation, and downstream analysis.

AbRefine: Framework-Conditioned Refinement for Structure-Guided Antibody CDR Design

AbRefine improves antibody CDR design by fusing structural and sequence predictions using framework context, achieving better recovery and lower log-likelihood than static fusion.

A Dimer-Seeded Pathway Governs the Nucleation of ProTα-H1 Biomolecular Condensates

This study reveals a dimer-seeded nucleation mechanism for ProTα-H1 biomolecular condensates using simulations and shows how electrostatic screening and protein supersaturation control nucleation and condensate properties.

A Structure-Aware Generative Framework for Exploring Protein Sequence and Function Space

This paper introduces a structure-aware generative framework that integrates geometric encoding and coevolutionary constraints to map, cluster, and design protein sequences, improving homology detection and structure-guided sequence generation.

EnsPlex: Integrative Protein Complex Prediction through Multi-source Complementary Structural Sampling and Topology-Aware Candidate Selection

EnsPlex improves protein complex structure prediction by integrating multi-source sampling and topology-aware candidate selection, achieving a 27.8% relative improvement over AlphaFold3 in antigen-antibody systems.

Network analysis of correlated conformational dynamics across the evolution of influenza A virus NS1

The paper analyzes the evolution of correlated conformational dynamics in influenza A virus NS1 proteins, revealing a core-periphery structure that enables evolutionary sequence variation while maintaining structural robustness.

Towards Generalizable Protein-ligand Co-folding with ACER

ACER improves protein-ligand co-folding by exploring alternative binding pockets and enhancing pose accuracy without retraining.

Ultrafast and Accurate Selection of High-Quality Protein Complex Models from Large-Scale Prediction

This paper introduces DeepUMQA-Selection, a framework for efficiently selecting high-quality protein complex models from large candidate pools, showing improved performance and speed.

SSAlign: Ultrafast and Sensitive Protein Structure Search at Scale

SSAlign improves protein structure search speed and sensitivity by using language models and a two-stage alignment strategy, outperforming Foldseek on large datasets.

Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes

The paper predicts quaternary structures of viral proteins using AlphaFold2 and AlphaFold-Multimer, identifying new insights into vaccinology and protease targets.

Decoding the Conformational Dynamics and Hyperactivity of Histone H3K36 N-Methyltransferase in Oncogenic Mutations via tICA and Markov State Modeling

This study uses molecular dynamics simulations to show that oncogenic NSD2 mutations enhance catalytic efficiency by reorganizing conformational dynamics rather than destabilizing the enzyme.

Probing Mechanisms of Allosteric Regulation in AAA+ ATPases for Microtubule Severing and Protein Disaggregation

This study investigates allosteric regulation mechanisms in AAA+ ATPases using katanin and ClpB, revealing similar and specific mechanisms through simulations and machine learning.

SOP-Multi-π: A Two-Site Coarse-Grained Model with Rescaled Aromatic Interactions to Bridge Single-Chain Ensembles and Condensate Phase Behavior of IDPs and Multidomain Proteins

The paper introduces SOP-Multi-π, a coarse-grained model with rescaled aromatic interactions to better simulate IDPs and their phase behavior in condensates.

SMartini: automated small molecule parametrization for Martini 3 force field

SMartini automates the creation of Martini 3 force field parameters for small molecules using molecular structures or SMILES strings, validated on drug-like compounds and metabolites.

Multi-Chain Hamiltonian Replica Exchange Framework for Probing Transient Helices and Order-Disorder Transitions in Proteins

This paper introduces a multi-chain Hamiltonian replica exchange framework to improve sampling of protein conformations, demonstrating its effectiveness in analyzing transient helices and order-disorder transitions in the IM30 protein.