Protein Structure and Dynamics

Trans-Allosteric Activation Releases Distinct Conformational Traps in Kinase Heterodimers

The paper introduces AlloQuant, a computational tool that quantifies kinase regulation by analyzing structural ensembles, and demonstrates its application to CDK1 and CSK to reveal distinct conformational mechanisms of activation.

GNMCADS: Sampling For Protein Conformation Diversity With Gaussian Network Model Guided Condition Annealed Diffusion Sampler

GNMCADS improves conformational sampling diversity by guiding diffusion models with Gaussian Network Model dynamics, outperforming existing methods on 92 proteins.

CD36 phosphorylation alters the thrombospondin binding site and reduces internal cavity accessibility and volume

This study uses computational methods to analyze how CD36 phosphorylation alters its structure, affecting TSP-1 binding and fatty acid uptake.

PathFold: Predicting the Entire Protein Folding Pathway from Protein Sequence Alone

PathFold predicts protein folding pathways from sequence using a deep learning framework combining AlphaFold and diffusion models, showing agreement with experimental data.

AlphaBridge: tools for the analysis of predicted biomolecular complexes

AlphaBridge evaluates predicted biomolecular complexes using AlphaFold3 confidence metrics, clustering sequence motifs, and visualizing interfaces with 2D diagrams and interactive tools.

Cross-taxon Coarse-Grained IDP Simulations Enable Architecture-Independent Generalization

The paper introduces BENDER, a dataset of IDP sequences across 13 taxonomic groups, and shows cross-taxonomic generalization of conformational ensemble predictions.

Design of peptides with non-canonical amino acids using flow matching

This paper introduces NCFlow, a generative model for designing peptides with non-canonical amino acids, showing improved binding affinity over existing methods.

Hashi: Bridging Statistical Model Derived 1D Microstate Encodings and Protein 3D Structural Ensembles

Hashi generates realistic protein structural ensembles from WSME model outputs, enabling rapid analysis of conformational states and functional insights.

Molecular Interactions of Viral Insulin/IGF-like Peptides with Zebrafish Receptors

This study uses molecular dynamics simulations to analyze how viral insulin/IGF-like peptides bind to zebrafish receptors, identifying conserved and unique interactions.

Universal physical principles of protein structural genesis emerge in language-model representation space

This paper identifies universal principles of protein structural emergence using language model representations, revealing three key principles and novel metrics for structural analysis.

Accurate and efficient prediction of protein conformations with ProtMonomer

ProtMonomer improves protein structure prediction accuracy and efficiency by combining models trained on diverse evolutionary information levels, outperforming AlphaFold2 and AlphaFold3 on challenging targets.

MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations

The paper introduces MOFF2, a transferable coarse-grained protein force field that improves simulation accuracy for various protein types and predicts condensate behavior.

ABAG-Rank: Improving Model Selection of AlphaFold Antibody-Antigen Complexes by Learning to Rank

ABAG-Rank improves model selection for AlphaFold3-predicted antibody-antigen complexes by learning to rank structural ensembles using geometric descriptors and confidence scores.

RegimeFormer: A Large Protein Model of Global Perturbation Regimes

RegimeFormer identifies protein perturbation regimes using a large-scale model and atlas, improving prediction accuracy and enabling downstream applications.

A thermodynamic framework for mapping elastic recoil mechanism across the human proteome

The paper develops a thermodynamic framework to classify elastic proteins by recoil mechanism using sequence-derived entropy estimates and identifies new candidates in the human proteome.

Towards transferable explicit-solvent coarse-grained models for biomolecular condensates

The paper improves a coarse-grained model for biomolecular condensates by enhancing dilute-state properties, showing better condensed-phase behavior but not full quantitative accuracy.

Prot2Surf: fast analysis of protein - surface binding modes

Prot2Surf analyzes and predicts protein-surface binding modes by calculating key features like distances and orientations, enabling efficient characterization of interaction patterns.

RPDynaFlow: Generating RNA-Protein Conformational Ensembles by Atomic Conditional Flow Matching

RPDynaFlow generates RNA-protein conformational ensembles using flow-matching, expanding phase space sampling beyond MD simulations for studying interactions.

Quantifying the binding affinity of a pharmacological chaperone to transient unfolded states of a normally folded protein

This study quantifies the binding affinity of a pharmacological chaperone to unfolded states of a normally folded protein using single-molecule force spectroscopy.

Local cooperative interactions reshape the folding transition in a one-dimensional spin-glass model

The paper uses a one-dimensional spin-glass model to show how local cooperative interactions affect protein folding stability and transition.

PMPNN-DDG: an accurate machine learning-based {triangleup}{triangleup}G prediction pipeline trained on a novel interpretable feature set extracted from ProteinMPNN

PMPNN-DDG is a Random Forest model predicting single-point mutation-induced protein stability changes using features from ProteinMPNN, achieving high accuracy on independent test sets.

Exploring protein conformational ensembles using evolutionary conditional diffusion

This paper introduces DiffEnsemble, a diffusion-based framework for modeling protein conformational ensembles, showing improved performance over existing methods.

WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

WaterFlow predicts ordered water molecule positions in protein structures with sub-angstrom accuracy, outperforming existing methods and improving drug design and crystallographic refinement.

Computational Structural Analysis of POLG Variants R627Q and W748S with Model-Variability Controls

This paper evaluates structural changes in POLG variants R627Q and W748S using AlphaFold2 models and experimental structures, finding no clear mutation-specific deformation but suggesting physicochemical hypotheses.

reactifpTM: an accessible reimplementation of actifpTM

reactifpTM reimplements actifpTM to calculate interface quality scores using standard outputs from model prediction software, showing strong correlation with actifpTM on a PDB dataset.

Inferring protein ensembles directly from NOESY spectra

The paper introduces a method to directly infer protein ensembles from NOESY spectra by combining quantitative scoring, regularized selection, and molecular dynamics.

Effect of Glycosylation on the Free Energy Landscape of the Catalytic Domain of Human Carbonic Anhydrase IX

This study uses molecular dynamics simulations to analyze how glycosylation affects the free energy landscape of HCA IX's catalytic domain in monomeric and dimeric forms, revealing increased landscape complexity with glycosylation.

Conformational ensembles of flexible multidomain proteins: How close are we to accurate and reliable predictions?

This study evaluates five computational methods for modeling conformational ensembles of flexible multidomain proteins using SAXS data, highlighting discrepancies and biases in their predictions.

A membrane insertion code for intrinsically disordered proteins

The paper identifies sequence determinants for aromatic residue insertion into membranes and develops a predictor model with high accuracy.

Enhanced sampling of protein conformations in AlphaFold3 with repulsive bias in the diffusion generative model

This paper improves AlphaFold3's ability to predict protein conformations by introducing a repulsive bias in its diffusion model, enabling better capture of ligand-induced structural changes.