Protein Structure and Dynamics

Molecular and Energetic Basis of Histidine Switch Dynamics in Respiratory Complex I

This study investigates the molecular and energetic basis of histidine switch dynamics in respiratory complex I using simulations, showing its coupling to lysine charge states and role in proton transfer.

A geometric atlas of how ESM3 organizes modalities across depth

The paper analyzes how ESM3, a multimodal protein language model, organizes different modalities across its depth, finding that physical modalities fuse into a shared subspace while functional annotations remain orthogonal.

Estimation of Absolute Protein-DNA Binding Free Energy using Streamlined Geometric Formalism

The paper estimates absolute protein-DNA binding free energy using a streamlined geometric formalism with high accuracy and low computational cost.

Benchmarking AI Protein Structure Predictors Reveals a Persistent Bias in Multi-State Proteins

This study benchmarks AI protein structure predictors on multi-state proteins, revealing persistent biases in capturing conformational ensembles and ligand interactions.

Protein stability is determined by single-site bias rather than pairwise covariance

The paper designs protein sequences with varying single-site biases and pairwise covariances, finding that single-site biases determine stability while pairwise covariances affect catalytic activity.

AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level

AF-CALVADOS uses AlphaFold to simulate multi-domain proteins at the proteome level, showing good performance across ordered and disordered regions.

Comparative Modelling of Actin-Tropomyosin Interfaces

This study models actin-tropomyosin interfaces using computational docking to analyze how filament length and isoform identity affect actin affinity across species.

IgGM2: An All-Atom Foundation Model for Adaptive Immune Receptor Design

IgGM2 is an all-atom foundation model for immune receptor design that jointly predicts CDR sequences and full-atom structures, outperforming existing methods in structure prediction and sequence design benchmarks.

Mind the Gap: An Embedding Guide to Safely Travel in Sequence Space

The paper introduces a hybrid method using a protein language model and Monte Carlo sampling to generate enzyme mutants that preserve structural features while varying overall sequence, providing sequences for experimental testing.

Long-Timescale Molecular Dynamics Reveal a Coordination-Biased Conformational Selection Mechanism for Sorcin Activation

This study uses long-timescale molecular dynamics simulations to show that Ca2+ binding shifts pre-existing active states in Sorcin rather than inducing activation de novo.

Adapting Co-Folding Models for Structure-Based Protein-Protein Docking Through Flow Matching

This paper adapts co-folding models for structure-based protein-protein docking by replacing their template module with a docking module and training with a flow-matching objective, showing competitive performance on specific targets.

Analysis and design of disordered polypeptides with optimized sequence patterning properties

This paper introduces a normalized sequence patterning framework for intrinsically disordered proteins and a design algorithm to generate sequences with desired phase separation properties.

Artificial intelligence aided design of peptides with custom secondary structure motifs and reduced amino acid alphabets

The paper designs peptides with custom secondary structures using a generative AI model trained on protein data, achieving success in creating novel proteins with desired motifs and reduced amino acid alphabets.

DynaPIN: A Tool for Characterizing Dynamic Protein Interfaces

DynaPIN extracts dynamic interface fingerprints from molecular simulations to better characterize protein interactions beyond static models.

ThermoFusion: A Multimodal Deep Learning Framework for Generalizable Prediction of Enzyme Thermostability

ThermoFusion predicts mutation-induced protein thermostability using a multimodal deep learning framework, showing strong performance on out-of-distribution sequences.

Conformation-Dependent Donor Selectivity in the Xanthan Gum Glycosyltransferase GumK Revealed by AI-Based Docking

This study uses AI-based docking and cofolding to show that GumK's donor selectivity depends on conformational states and ligand interactions, not a single rigid binding mode.

PEPstrMOD2: Next-generation tertiary structure prediction of chemically modified and non-natural peptides

PEPstrMOD2 improves peptide structure prediction by using deep learning and expanding chemical modifications support, outperforming previous methods on benchmark datasets.

The Influence of Ligands on AlphaFold3 Prediction of Cryptic Pockets

This study evaluates AlphaFold3's ability to predict cryptic pockets and their ligand binding, showing it can generate accurate structural ensembles when provided with ligands.

OpenCafeMol with 3SPN.2 DNA model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations

The paper extends a GPU-accelerated molecular dynamics simulator to support DNA models and improves efficiency for simulating chromatin interactions over long timescales.

Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition

This study benchmarks AlphaFold and related methods for modeling antibody and TCR antigen recognition, showing improvements with AlphaFold3 and increased sampling but varying success across complex types.

Beyond additivity: zero-shot methods cannot predict impact of epistasis on protein properties and function

The paper evaluates zero-shot models' ability to predict epistatic effects on protein properties and finds they fail to predict strongly epistatic mutation combinations.

Solvent-buffer effects in molecular dynamics simulations of nucleic acids

This study investigates how simulation cell size affects nucleic acid dynamics by comparing different solvent-buffer distances in molecular dynamics simulations.

A generalisable framework to inject distance information into Alphafold-like structure predictors

This paper introduces a method to inject distance information into AlphaFold-like structure predictors to improve structure prediction accuracy.

An Atlas of Short Linear Motif-Mediated Human Protein-Protein Interactions

The paper maps over 20,000 human protein-protein interactions mediated by short linear motifs using a peptide library screening approach.

Accurate ΔTm Prediction Without Protein Structure Inputs for Biomolecular Stability

The paper shows that accurate ΔTm prediction can be achieved using a sequence-only model without structural inputs, outperforming structure-informed methods.

Conformational changes induced in ubiquitin by circular protein-DNA chimeras

This study uses circular protein-DNA chimeras to investigate conformational changes in ubiquitin induced by DNA attachment, showing that local DNA-protein interactions drive structural shifts.

GTcomplex: Spatial indexing-powered search and alignment of macromolecular complexes

GTcomplex improves structural alignment of macromolecular complexes by directly aligning entire complexes rather than individual chains, achieving higher accuracy and speed.

AlphaFold Database expands to proteome-scale quaternary structures

The paper expands the AlphaFold Protein Structure Database to include proteome-scale quaternary structures, predicting 1.81M high-confidence protein complexes and revealing conserved structural clusters across domains of life.

Expanding all-α-helical protein space through rational computational design

The paper designs de novo all-α-helical proteins using computational methods and validates their stability and structure.

Biomolecular Condensation and L-Cysteine Signaling Activates Dormant Protease Activity of Papain Droplets: Implication toward Meat Tenderization

This study shows that papain's protease activity is regulated by biomolecular condensation and L-cysteine, leading to dormant and reactivated states with implications for meat tenderization.