mixed model

Structural and Energetic Determinants of Monobody Recognition of Oncogenic KRAS Variants

This study identifies structural and energetic determinants of monobody 12D4 recognition of KRAS variants using simulations and redesign, revealing key interactions and mutations for improved selectivity.

Identification and targeting of a novel drug pocket in the tumour angiogenesis regulator RhoJ

This study identifies a novel allosteric pocket in RhoJ and shows that terconazole binds to it, disrupting its interaction with PAK3.

Danuglipron and orforglipron engage GLP-1R through materially different interfaces: an unbiased molecular dynamics study

This study uses molecular dynamics to show that danuglipron and orforglipron bind GLP-1R through distinct interfaces, with different contact distributions and occupancy patterns.

Structural basis of selective phospholipid recognition and local membrane deformation by CTL1

This study identifies CTL1 as a phospholipid-binding protein that deforms membranes, revealing its structural basis and potential role in phospholipid homeostasis.

Molecular determinants of ligand recognition and efficacy in the TRPM3 voltage sensor-like domain

This study identifies molecular determinants of ligand recognition and efficacy in TRPM3's voltage sensor-like domain using a combination of structural and functional analyses.

Computational Structure Modeling, Functional Characterization, and Identification of Potential Inhibitors for the cyclic-di-GMP Mediated Biofilm Forming Membrane Protein in Vibrio cholerae

This paper identifies natural inhibitors of a membrane protein involved in biofilm formation in Vibrio cholerae through structural modeling, functional analysis, and virtual screening.

From Structure to Dynamics: Activation Mechanism of the G Protein-Coupled Bile Acid Receptor 1-Gs Complex

This study investigates how lithocholic acid modulates GPBAR1 activation and G protein engagement through molecular dynamics simulations and structural analysis.

A Preparation-Free Mixture-of-Experts Framework for Protein-Ligand Affinity Prediction

This paper introduces HydrAffinity, a mixture-of-experts model for protein-ligand affinity prediction that outperforms interaction-free methods and matches state-of-the-art interaction-based methods.

Elevated conformational dynamics makes ACKR3 activation-prone and G protein-incompetent

This study compares the conformational dynamics of ACKR3 and CXCR4 using MD simulations and BRET assays, revealing that ACKR3's dynamic behavior leads to activation-proneness and G protein-incompetence.

Ligandability Assessment of the LAG-3 D1 Domain Enables Discovery of a Small-Molecule Inhibitor

The paper assesses the ligandability of the LAG-3 D1 domain using molecular dynamics, virtual screening, and biochemical assays, identifying a small-molecule inhibitor with micromolar affinity.

Computational Prediction of Plasmodium falciparum Antigen-T-cell Receptor Interactions via Molecular Docking: Implications for Malaria Vaccine Design

This study uses molecular docking to predict Plasmodium falciparum antigen-T-cell receptor interactions, identifying three antigens as potential vaccine candidates.

Elucidating the conformational dynamics of the mitochondrial localization signal, M3, of TDP-43 and accessing potential inhibitors using molecular docking and simulation

This study identifies vitamin D3 as a potential inhibitor of TDP-43's mitochondrial mis-localization through molecular docking and simulation of the M3 region.

Predicting non-covalent interactions between antioxidants in biological membranes through molecular dynamics

This study uses molecular dynamics to predict non-covalent interactions between antioxidants in lipid bilayers, validating MD simulations as a tool for assessing antioxidant synergism.

Aggregation-Prone Region Mapping in Olfactomedin Domain of Myocilin through Classical and Enhanced Sampling Molecular Dynamics Simulations

This study maps aggregation-prone regions in the myocilin OLF domain using molecular dynamics simulations to identify potential therapeutic targets for POAG.

Structural and dynamic study of fungal cell wall degrading fungal chitinase and its interaction with chitooligosaccharide

This study uses molecular modeling and simulation to analyze the structure and dynamics of a fungal chitinase and its interaction with chitotriose, revealing key residues and stability mechanisms.

Ammonia-mediated Conformational Dynamics in SCAP for SREBP Activation

This study uses molecular dynamics simulations to show ammonia induces conformational changes in SCAP that activate the SREBP pathway by promoting dissociation from Insig.

REV-ERBβ Binding Pocket Dynamics with Implications for Rational Design of Small Molecule Modulators

This study uses molecular dynamics simulations to analyze REV-ERBβ ligand-binding domain dynamics and antagonist effects on NCoR peptide binding, informing rational drug design.

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

This study presents near-physiological structures of the Fc fragment from a biosimilar VEGF-Trap and shows structural plasticity through molecular dynamics simulations.

Disrupting Viral Replication in Human Metapneumovirus: Targeting Key Proteins with Unani Phytochemicals through Structural Dynamics and Energetics

This study evaluates Unani phytochemicals against HMPV using computational methods, finding strong binding affinities and stability for Crocin, Quercetin, and Oleuropein.

Assessing the helical stability of polyXYs at the boundaries of Intrinsically Disordered Regions with MD simulations

The paper uses MD simulations to study helical stability in polyXY sequences at IDR boundaries, finding they form dynamic helices that may aid in protein flexibility.

A Molecular Dynamics Protocol for Rapid Prediction of EGFR Overactivation and Its Application to the Rare Mutations S768I, S768N, D761N

This paper develops a molecular dynamics protocol to predict EGFR mutation effects and applies it to three rare mutations, showing how they alter structural dynamics and activity.

Structural conformations of intrinsically disordered proteins of podocyte slit-diaphragm

The paper investigates the structural dynamics of slit-diaphragm proteins using molecular docking and simulations, revealing conformational adaptations and subunit-sharing mechanisms in health and disease.

Insights from Molecular Docking and Dynamics Simulations of P2RX7-????Syn Complex

This paper uses molecular docking and dynamics simulations to study the interaction between P2RX7 and alpha-synuclein, identifying binding sites and structural changes involved in neuronal damage.

Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics

This study uses Gaussian accelerated MD simulations to improve tunnel sampling in enzymes, revealing new transient tunnels and their functional relevance.

Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models

This study uses molecular dynamics simulations and AlphaFold2 models to investigate MfgE8 conformations and how they affect medin cleavage site accessibility.

Atomic insights into the signaling landscape of E. coli PhoQ Histidine Kinase from Molecular Dynamics simulations

The paper uses Molecular Dynamics simulations and AlphaFold2 to study PhoQ signaling, revealing three conformations and insights into its activation mechanism.

Investigating the Structural Impact and Conformational Dynamics of a Sequence Variant (c.242G>A) in TMIE Gene Provoking Usher Syndrome

This study uses molecular dynamics simulations to show that the c.242G>A variant in TMIE causes structural instability and conformational changes leading to Usher syndrome.

Molecular dynamics of outer membrane-embedded polysaccharide secretion porins reveals closed resting-state surface gates targetable by virtual fragment screening for drug hotspot identification

The paper uses molecular dynamics to study porin structures and identifies drug targets for inhibiting polysaccharide secretion.

A Conserved Electrostatic Membrane-Binding Surface in Synaptotagmin-Like Proteins Revealed Using Molecular Phylogenetic Analysis and Homology Modeling

The paper uses molecular phylogenetic analysis and homology modeling to show that the electrostatic membrane-binding surface of synaptotagmin-like proteins is highly conserved across vertebrates.

Molecular Dynamics and Water site bias docking method allows the identification of key amino acids in the Carbohydrate Recognition Domain of a viral protein

The paper introduces a computational method combining molecular docking and dynamics simulations to identify key amino acids in a viral protein's Carbohydrate Recognition Domain, validated by in vitro experiments.