mechanistic / dynamical model

This study uses Molecular Dynamics simulations to compare ion and water permeability of Cldn10b and Cldn15 paracellular channels, revealing structural determinants of their permeability properties.

This study evaluates force field limitations in constant pH molecular dynamics simulations of a mini-protein, showing significant pKa errors due to force field and water model choices.

This paper introduces AlphaFold-Metainference to predict structural ensembles of disordered proteins using AlphaFold-derived distances in molecular dynamics simulations.

The paper investigates how anchor point selection affects the mechanical stability of an Affibody/PD-L1 complex using multiple experimental and computational methods.

This study investigates how an amyloidogenic peptide binds to DNA, showing its structural interactions and effects on DNA function.

This study shows that NOLC1 suppresses cisplatin chemotherapy and immune checkpoint inhibitor therapy in gastric cancer by inhibiting p53-mediated ferroptosis.

This paper uses molecular dynamics simulations to show that cholesterol stabilizes M2 channel clusters, enhancing membrane curvature and promoting viral budding.

This study uses molecular dynamics simulations to design HIV-1 immunogens that select for specific mutations in broadly neutralizing antibodies.

This study uses molecular dynamics simulations to investigate how H3/H4 tetramers are recycled during DNA replication in yeast, revealing pathways and regulatory factors involved in strand-specific recycling.

The paper uses single-molecule imaging and molecular dynamics simulations to study early MET receptor activation in situ, revealing structural dynamics and a refined dimer model.

This study investigates dopamine receptor-ligand interactions using molecular modeling, revealing binding modes and stability of agonists and antagonists at D1R and D5R.

This study identifies polyphosphate as the 'mystery density' in α-synuclein fibrils by showing it binds to lysine residues, affecting fibril formation and toxicity.

This study uses molecular dynamics to compare Cu2+ and Mg2+ binding to Dickerson DNA, revealing similar binding preferences but distinct binding mechanisms for Cu2+.

This study shows membrane tension drives NINJ1 filament opening, causing cell lysis, and explains why NINJ2 fails to form lesions.

IsRNAcirc predicts circular RNA 3D structures using coarse-grained molecular dynamics, outperforming template-based methods on a validation set.

This study uses molecular dynamics simulations to analyze ligand escape pathways and conformational stability in LIV-binding protein, identifying two distinct pathways and the role of water in the process.

This study resolves a discrepancy in aromatic amino acid sticker strength by showing tyrosine is stronger in condensates due to lower transfer free energy, but this reverses in apolar media.

This study investigates A22's interactions with prokaryotic MreB and eukaryotic actin using computational and experimental methods, revealing strong binding and toxicity to eukaryotic cells.

This study uses molecular dynamics to analyze inhibitor binding to DHFR, showing that reduced activity correlates with multiple-bound states on the protein surface.

This study uses molecular dynamics simulations to investigate how phosphorylation patterns and salt concentration affect RNA Polymerase II CTD clustering behavior.

This paper develops a physical model of the endoplasmic reticulum as an active liquid network to explain its dynamic structure and function.

This study uses statistical coupling analysis and molecular dynamics to show that dynamically coupled residues in DHFR influence evolution and allosteric communication.

This study identifies TET2-mutant clonal hematopoiesis in thyroid cancer microenvironments and shows that TGFβ signaling from these macrophages mediates resistance to BRAF/MEK inhibition, with TGFβ inhibition restoring sensitivity.

This study investigates how oxidation of histone H3 cysteines affects nucleosome structure using molecular modeling, revealing mechanisms and structural consequences of S-sulfenylation.

This study compares lipid nanoparticles in Pfizer-BioNTech and Moderna COVID-19 vaccines using molecular dynamics simulations, finding differences in ionizable lipid structure that may explain storage temperature differences.

This study identifies two mutation profiles in EGFR Exon-19 deletions that correlate with differential TKI sensitivity through analysis of conformational dynamics and solvent interactions.

This paper shows EGCG inhibits TDP-43 aggregation and cytotoxicity in vitro through binding to its C-terminal domain.

The paper develops a model of human stepping regulation that integrates mechanical and motor templates to explain semistable walking patterns observed in experiments.

This paper uses molecular dynamics simulations to study ion dynamics in PDDA-ATP coacervates, showing that transferring to DI water causes ion ejection and structural changes that stabilize the coacervates.

This study uses computational methods to analyze Zn2+-mediated non-competitive inhibition of caspase-3, revealing atomic-level insights into its mechanism and potential therapeutic applications.