mechanistic / dynamical model

This study models the structure and simulates the membrane binding and pore formation mechanism of PfPLP1, revealing how it interacts with host cell membranes and forms pores.

This study shows breast tumors sustain growth by manipulating adipocytes into pre-adipocytes through RET signaling, which promotes tumor progression.

The paper tests if molecules from ultra-large libraries are more selective than those from bio-like libraries, finding similar off-target activity despite differences in chemical novelty.

This study identifies HrpZ2 interactors in tomato aquaporins through molecular docking and MD simulations, showing PIPs as primary targets and TIPs/NIPs as auxiliary partners.

The paper identifies a tick saliva protein that specifically binds to Borrelia burgdorferi lipids, suggesting a potential role in pathogen recognition.

The paper shows that amyloid formation in PACAP-family peptides is controlled by heparin-sensitive lysine/arginine residues, conserved across evolution despite sequence divergence.

This study shows DNA supercoiling affects GCN4-DNA binding stability and conformational dynamics through experimental and simulation approaches.

This study evaluates TRPC6 missense variants in cancer patients using molecular docking and patch clamp electrophysiology to predict functional impact and guide clinical decisions.

The paper identifies KLP-6 as a kinesin-3 resistant to ADP inhibition, showing its unique ATP selectivity through sequence and molecular dynamics analysis.

This study identifies small molecules that inhibit c-MET activity by targeting its extracellular domain, showing reduced cell viability and autophosphorylation in HCC cells.

This study uses molecular dynamics simulations to show how respiratory aerosols create structured microenvironments that influence SARS-CoV-2 stability and spike dynamics.

This study identifies a novel allosteric site on the mu-opioid receptor using cryo-EM and MD simulations, revealing a lipid-sensitive mechanism for positive allosteric modulation.

This study shows that LIPT1 loss causes replication stress and PARP inhibitor sensitivity via PrimPol-mediated ssDNA gaps in cancer cells.

This study identifies hnRNP C as a repressor of circRNA biogenesis in Group 3 medulloblastoma by binding Alu elements and preventing pre-mRNA circularization.

This study investigates the gating mechanism of MthK channels using mutants, revealing hydrophobic and lipid-mediated processes that drive channel closure.

This paper introduces a two-point neuron model to simulate how contextual information is integrated in visual processing, showing how apical-basal integration supports coherent signal amplification and learning.

This study identifies the mechanical basis of coordinated chromosome motion during metaphase using live-cell imaging, perturbations, and a minimal mechanical model.

The paper identifies water-contact residues in GerAB that are critical for germinosome stability in Bacillus subtilis spores, based on MD simulations and functional assays.

This paper develops a framework linking molecular thermodynamics to macroecological patterns of range expansion, showing that adaptation to warmer temperatures is easier than to cold.

This paper designs, synthesizes, and evaluates new acid-functionalized carbazole derivatives as potential antibiotics, showing strain-specific antibacterial activity and favorable pharmacokinetic properties.

This paper presents a continuous biomanufacturing platform for virus-like particle vaccines using multiple bioreactor configurations, demonstrating stable production and scalability.

This study investigates how 18:0 and 18:1 lysophosphatidic acids bind and activate LPA1 receptor differently using molecular dynamics simulations.

This study uses molecular dynamics simulations to show that ribosome crowding in polysomes causes mRNA to transition from 3D to quasi-2D structure, altering its scaling behavior and conformation.

This study uses molecular dynamics simulations to investigate how vitrification affects the conformational ensemble of Trp-cage miniprotein and develops a thermodynamic inference framework to recover equilibrium populations from vitrified samples.

This paper develops mechanistic ODE models to predict Valley fever outbreaks by integrating climate and ecological factors, showing improved forecasting over statistical models when including wildlife reservoirs.

This study uses molecular dynamics simulations to show that SMC complexes translocate DNA unidirectionally by capturing DNA segments and pumping them through an asymmetric kleisin path.

This paper identifies CACNA1C as a prognostic biomarker and therapeutic target in high-grade serous ovarian cancer, showing nifedipine suppresses tumor growth through calcium channel blockade.

This study investigates how the R39C mutation in sialin affects its lysosomal transport function by analyzing structural and dynamic changes in the protein.

The paper uses molecular dynamics simulations to reveal the unique architecture of the mycobacterial outer membrane, showing fluid outer leaflets and ordered inner leaflets that contribute to bacterial resilience.

This study analyzes the free energy and flexibility of autoinhibited human BRAF using molecular dynamics simulations based on a cryo-EM model to understand its activation mechanism.