structural biology

Mapping the brain-web morphology to characterise ageing and cognitive impairment

This paper introduces SHARP, a method using cosmological web analysis to characterize brain ageing and cognitive impairment by analyzing MRI data from CamCAN and OASIS-3.

LinearKnot: linear-time ensemble analysis of RNA density-2 pseudoknots under hierarchical folding

LinearKnot approximates CParty's hierarchical pseudoknot analysis with linear time complexity, achieving comparable accuracy for RNA structure prediction and ensemble calculations.

A cohesin acetylation complex that recognises nicked DNA

The paper predicts a cohesin acetylation complex in budding yeast that interacts with nicked DNA and confirms its function through experiments.

FoXSight: Facilitating Computational Hit Identification in Crystallographic Fragment Screening Experiments

FoXSight identifies weak binding events in crystallographic fragment screening by detecting target-specific density features in noisy electron density maps.

A validation approach for RNA structures based on deep-learning 3D-structure predictions

This paper extends a protein structure validation method to RNA, showing it can detect errors in low-resolution structures where map-based methods fail.

Long-range allosteric restraint by the Spiral-Pincer scaffold gates oxidative activation of the ATM kinase

The paper investigates how the Spiral-Pincer scaffold regulates ATM kinase activation by oxidative stress, showing it restricts access to an oxidation-competent conformation.

Lesion-Derived Estimated Functional and Structural Connectomes Predict Post-Stroke Recovery Outcomes

The paper develops a pipeline to estimate structural and functional connectomes from lesion masks to predict post-stroke recovery outcomes, showing better performance than traditional methods.

BundleMorphometry: Spatially Resolved White Matter Bundle Shape Analysis Using Nonlinear Streamline-based Registration

BundleMorphometry quantifies local white matter bundle shape using nonlinear registration, revealing deformation patterns in glioma and Parkinson's disease datasets.

EigenBrain maps cortical molecular architecture from functional, geometric, and structural eigenmodes

The paper shows functional MRI eigenmodes can approximate specific receptor and transporter distributions in the cortex, while structural and geometric eigenmodes cannot, and applies this to detect molecular differences in autism and schizophrenia.

Decoding antibody-antigen recognition: the BL8 language and its application in calibrating deep learning predictions

This paper introduces BL8, a structural language to evaluate deep learning predictions of antibody-antigen interactions, revealing false positives and enabling reliable consensus predictions.

A directed TM->JM coupling in receptor tyrosine kinase dimers, set by activating mutations and the membrane environment

The paper uses MD simulations and computational methods to determine the direction of conformational coupling in RTK dimers, showing it correlates with receptor activity states.

DSSNA: Automated Nucleic Acid Structure Analysis in Molecular Dynamics

DSSNA v2026 analyzes nucleic acid structures in MD simulations, identifying base pairs, hydrogen bonds, and stacking interactions, showing that canonical pairs are stable while non-canonical ones are transient.

Mechanism of GPR84 allosteric modulation at a helix 8-proximate site

This paper identifies a helix 8-proximate allosteric site in GPR84 and shows how it enables Gi-biased signalling through structural and dynamic mechanisms.

Temporal Hydrogen-Bond Network Analysis Reveals Substrate-Directed Connectivity in Dihydrofolate Reductase

The paper introduces a temporal hydrogen-bond network analysis framework to study ligand-directed connectivity in DHFR, revealing mutation-sensitive pathways and evolutionarily supported communication regions.

Interrogating contrastive learning embeddings for structure-based virtual screening: a case study on DrugCLIP

This paper evaluates DrugCLIP's contrastive learning embeddings for virtual screening, showing strong performance but limitations under realistic conditions.

Mechanistic Dissection of Conformational Transition of Bicyclic Peptide via Molecular Modeling and Deep Learning

This study introduces a deep learning model to analyze conformational transitions in cyclic peptides, revealing key residues and nonlinear torsional motions that govern structural changes.

Conformational Ensembles of the Disordered 4E-BP2:eIF4E Complex Restrained by smFRET Experiments

The paper generates conformational ensembles of the 4E-BP2:eIF4E complex using smFRET and NMR data, revealing dynamic structural changes and new contact regions.

Substrate binding reorganizes the energetic landscape of Plasmodium falciparum hexose transporter PfHT1

This study shows how glucose binding reorganizes the conformational and energetic landscape of PfHT1, a malaria parasite transporter, using computational methods and experimental validation.

Predicting Capsid Protein Binding Sites in Single-Stranded RNA Viruses Using Machine Learning from Local Geometric Features

This paper develops a machine learning framework to predict capsid protein binding sites in ssRNA viruses using local geometric features from RNA structures, achieving high accuracy with and without experimental data.

Structural basis of lipid-mediated self-regulation of Tissue Factor.

This paper identifies two lipid-mediated mechanisms of Tissue Factor self-regulation through structural analysis, revealing conformational changes and their impact on FVII binding.

Phosphoinositides protonation states dictate AKT1 binding with membrane

This study shows that phosphoinositide protonation microstates determine AKT1 membrane binding specificity and how mutations alter this interaction.

Mechanochemical Decoupling of ATP Hydrolysis and RNA Translocation in SARS-CoV-2 nsp13 by the L405D Mutation

This paper investigates how the L405D mutation in SARS-CoV-2 nsp13 decouples ATP hydrolysis from RNA translocation by altering conformational dynamics.

Synergistic Effects of pH and Temperature on Dengue VirusEnvelope Dimers: Insights from Microsecond MolecularDynamics Simulations

This study uses molecular dynamics simulations to show how pH and temperature together destabilize dengue virus envelope dimers, revealing a 'compensatory embrace' mechanism and potential targets for antiviral drugs.

Structures of pUG-fold RNA bound to DNMT1 reveal a mechanism for RNA-mediated epigenetic regulation

This study determines the cryo-EM structures of DNMT1 bound to pUG-fold RNA, revealing two RNA-binding modes and their role in inhibiting DNMT1 activity.

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.

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.

A novel lipid-triggered allosteric site modulates LC3-LIR receptor binding activity

This study identifies a lipid-triggered allosteric site in LC3 that modulates receptor binding activity through conformational changes upon membrane engagement.

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.

Ligand Binding Kinetics, Thermodynamics, and Gating of Insect Odorant Receptor

This study investigates the ligand binding kinetics, thermodynamics, and gating of the insect odorant receptor MhOR5 using molecular dynamics simulations, revealing key structural determinants and differences in ligand behavior.

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.