mixed model

Optimization of the NFκB-DNA ensemble leads to high affinity binding of partial consensus sites

The paper investigates how NFκB (RelA/p50) achieves high-affinity binding to partial consensus DNA sequences through structural rearrangements and dynamic interactions.

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.

DeepD enables efficient genome modeling and controllable long-context sequence generation across domains of life

DeepD is a genome foundation model that enables accurate sequence-to-function prediction and controllable genome-scale sequence generation across domains of life.

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.

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.

OmniGene-4: A Unified Bio-Language MoE Model with Router-Level Interpretability

OmniGene-4 is a multi-modal bio-language MoE model that decomposes task performance by router states, achieving strong benchmarks in homology and biological-knowledge tasks while being computationally efficient.

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.

Structure-Guided Biochemical Design of DNA Tweezers As A Dual Target of the Primary Glioblastoma Biomarkers S100A4 and Midkine

This study designs DNA tweezers that selectively bind S100A4 and midkine, biomarkers of glioblastoma invasiveness, using computational methods and molecular docking.

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.

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.

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.

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.

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.

Mixture of Experts Enable Efficient and Effective Protein Understanding and Design

AIDO.Protein is a mixture-of-experts model for protein understanding and design, achieving state-of-the-art performance with improved efficiency.

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.

PIPI-C: A combinatorial optimization framework for identifying post-translational modification crosstalks in mass spectrometry data

PIPI-C identifies PTM crosstalks in mass spectrometry data using a combinatorial optimization framework, revealing upregulated PTM patterns in cancer datasets.

Impact of aging on the GABAB receptor-mediated connectome

This paper investigates how aging affects GABAB receptor interactions and membrane lipid composition in rat cerebella, revealing reduced GABAB2 expression and altered lipid profiles that impact protein-protein interactions.

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.

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.

A computational investigation on Rho-related GTP-binding protein RhoB through molecular modeling and molecular dynamics simulation study

This study predicts the structure of RhoB using molecular modeling and simulates its dynamics to identify key residues involved in stability and function.

Insulin docking within the open hemichannel of connexin 43 may reduce risk of amyotrophic lateral sclerosis

The paper investigates how insulin interacts with connexin 43 hemichannels and suggests this interaction may reduce ALS risk by blocking toxic substance transfer.

In silico conformational features of botulinum toxins A1 and E1 according to the intraluminal acidification

This study uses molecular dynamics simulations to analyze conformational changes in botulinum toxins A1 and E1 under different pH conditions, revealing domain movements and structural dynamics.

Molecular dynamics analysis of fast-spreading severe acute respiratory syndrome coronavirus 2 variants and their effects in the interaction with human angiotensin-converting enzyme 2

The paper uses molecular dynamics simulations and SPR assays to analyze how SARS-CoV-2 variants bind to the ACE2 receptor and how this affects viral spread.