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dynamics simulation (mds) results  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc dynamics simulation (mds) results
    Dynamics Simulation (Mds) Results, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/md+simulation+results/dynamics++md++simulation+results/pmc11509260-281-17-18
    Average 90 stars, based on 1 article reviews
    dynamics simulation (mds) results - by Bioz Stars, 2026-11
    90/100 stars

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    Solvent:

    Article Title: Atomistic Modeling of Functionalized Magnetite Surfaces with Oxidation States.
    Article Snippet: In a recent study a reparameterization of the Lennard−Jones (LJ) parameters for the adsorbate oxygen atoms was suggested, which improved those bond lengths but might limit transferability and Figure 4. (a) Energy difference between oxidation state minimized (min) and layered (layer) structures at full coverage with respect to surface thickness, at “tet” and “int” binding sites. (b) Binding site preference at half coverage for minimized and Molecular Dynamics (MD) resulted structures with respect to surface thickness.

    Article Title: Bile Salt Induced Aggregation and Nanostructure Formation of β-Lactoglobulin in Gastrointestinal Environments
    Article Snippet: β-Lactoglobulin (BLG) is an important food protein with great nutritional value.. It exists as monomeric and dimeric forms at pH 3.0 (gastric conditions) and 6.2 (small intestine conditions), respectively.. The structural stability of BLG at acidic pH prevents its denaturation in the stomach.

    Article Title: Neuropilin-1 promotes mitochondrial structural repair and functional recovery in rats with cerebral ischemia
    Article Snippet: Fig. 9 The analysis of Molecular Dynamics Simulation (MDS) results.

    Article Title: Mpropred: A machine learning (ML) driven Web-App for bioactivity prediction of SARS-CoV-2 main protease (Mpro) antagonists.
    Article Snippet: Molecular dynamics (MD) simulation results The RMSD of backbone atoms of the protein-ligand complexes were analyzed to view their stability.

    Article Title: Mesothelin- and nucleolin-specific T cells from combined short peptides effectively kill triple-negative breast cancer cells
    Article Snippet: Molecular dynamics (MD) simulation outcomes demonstrated the distances between the second and ninth amino acid residues, which were 15.079 angstroms (Å) for pM-01, 17.833 Å for pM-02, 20.772 Å for pN-01, and 19.144 Å for pN-02 (Fig. A).

    Article Title: Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis.
    Article Snippet: Sample % Hemolysis LF 38.5 ± 0.7 LF + P1 0.5 ± 0.09 LF + P1-VF 1.8 ± 0.04 LF + P1-FF 1.1 ± 0.08 LF + P1-LVF 1.4 ± 0.08 LF + P1-LVFF 1.8 ± 0.19 LF + P2-VF 0.26 ± 0.08 LF + P2-FF 0.26 ± 0.05 LF + P2-LVF 0.21 ± 0.16 LF + P2-LVFF 0.15 ± 0.06 Molecular dynamics (MD) simulation results.

    Article Title: Molecular Mechanics of Liquid and Gas Slip Flow
    Article Snippet: Molecular dynamics (MD) simulation results and associated uncertainty (for βGK) are depicted with blue dots, and the prediction of Equation 51 and associated uncertainty are depicted with the dark red line and light-red shading, respectively.

    Article Title: Non-Nucleoside Lycorine-Based Analogs as Potential DENV/ZIKV NS5 Dual Inhibitors: Structure-Based Virtual Screening and Chemoinformatic Analysis
    Article Snippet: XP glide docking pose and 2D diagram of the interaction results of lycorine enantiomers; Figures S9 and S10: Molecular dynamics simulation (MDS) results of DENV3 and ZIKV RdRp–ligand complex; Figures S11 and S12: Comparative MD simulation results at 500 ns timescale of DENV and ZIKV NS5 RdRP proteins in complex with LYCR and LYCS ligands.

    Binding Assay:

    Article Title: Atomistic Modeling of Functionalized Magnetite Surfaces with Oxidation States.
    Article Snippet: In a recent study a reparameterization of the Lennard−Jones (LJ) parameters for the adsorbate oxygen atoms was suggested, which improved those bond lengths but might limit transferability and Figure 4. (a) Energy difference between oxidation state minimized (min) and layered (layer) structures at full coverage with respect to surface thickness, at “tet” and “int” binding sites. (b) Binding site preference at half coverage for minimized and Molecular Dynamics (MD) resulted structures with respect to surface thickness.

    Article Title: Bile Salt Induced Aggregation and Nanostructure Formation of β-Lactoglobulin in Gastrointestinal Environments
    Article Snippet: β-Lactoglobulin (BLG) is an important food protein with great nutritional value.. It exists as monomeric and dimeric forms at pH 3.0 (gastric conditions) and 6.2 (small intestine conditions), respectively.. The structural stability of BLG at acidic pH prevents its denaturation in the stomach.

    Article Title: Neuropilin-1 promotes mitochondrial structural repair and functional recovery in rats with cerebral ischemia
    Article Snippet: Fig. 9 The analysis of Molecular Dynamics Simulation (MDS) results.

    Article Title: Mpropred: A machine learning (ML) driven Web-App for bioactivity prediction of SARS-CoV-2 main protease (Mpro) antagonists.
    Article Snippet: Molecular dynamics (MD) simulation results The RMSD of backbone atoms of the protein-ligand complexes were analyzed to view their stability.

    Article Title: Mesothelin- and nucleolin-specific T cells from combined short peptides effectively kill triple-negative breast cancer cells
    Article Snippet: Molecular dynamics (MD) simulation outcomes demonstrated the distances between the second and ninth amino acid residues, which were 15.079 angstroms (Å) for pM-01, 17.833 Å for pM-02, 20.772 Å for pN-01, and 19.144 Å for pN-02 (Fig. A).

    Article Title: Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis.
    Article Snippet: Sample % Hemolysis LF 38.5 ± 0.7 LF + P1 0.5 ± 0.09 LF + P1-VF 1.8 ± 0.04 LF + P1-FF 1.1 ± 0.08 LF + P1-LVF 1.4 ± 0.08 LF + P1-LVFF 1.8 ± 0.19 LF + P2-VF 0.26 ± 0.08 LF + P2-FF 0.26 ± 0.05 LF + P2-LVF 0.21 ± 0.16 LF + P2-LVFF 0.15 ± 0.06 Molecular dynamics (MD) simulation results.

    Article Title: Molecular Mechanics of Liquid and Gas Slip Flow
    Article Snippet: Molecular dynamics (MD) simulation results and associated uncertainty (for βGK) are depicted with blue dots, and the prediction of Equation 51 and associated uncertainty are depicted with the dark red line and light-red shading, respectively.

    Article Title: Non-Nucleoside Lycorine-Based Analogs as Potential DENV/ZIKV NS5 Dual Inhibitors: Structure-Based Virtual Screening and Chemoinformatic Analysis
    Article Snippet: XP glide docking pose and 2D diagram of the interaction results of lycorine enantiomers; Figures S9 and S10: Molecular dynamics simulation (MDS) results of DENV3 and ZIKV RdRp–ligand complex; Figures S11 and S12: Comparative MD simulation results at 500 ns timescale of DENV and ZIKV NS5 RdRP proteins in complex with LYCR and LYCS ligands.



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