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two-component coarse-grained molecular-dynamics model  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc two-component coarse-grained molecular-dynamics model
    Two Component Coarse Grained Molecular Dynamics Model, 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/dynamic+component+model/pm26525932-198-2-6?v=Molecular+Dynamics+Inc
    Average 90 stars, based on 1 article reviews
    two-component coarse-grained molecular-dynamics model - by Bioz Stars, 2026-08
    90/100 stars

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    Image Search Results


    Specific chemical formulae for the first 15 active compounds. From ( A – O ) are Sexangularetin, DFV, Jaranol.naringenin.6-prenylated eriodictyol, Quercetin der., Glabridin, Sigmoidin-B, licoisoflavanone, glyuranolide, 7,2’,4’-trihydroxy–5-methoxy-3–arylcoumarin, isorhamnetin, kanzonols W, Karanjin, Delphin_qt. Protein-protein interaction (PPI) network depicting the interactions of SND-related proteins involved in UC treatment.

    Journal: Journal of Inflammation Research

    Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

    doi: 10.2147/JIR.S516556

    Figure Lengend Snippet: Specific chemical formulae for the first 15 active compounds. From ( A – O ) are Sexangularetin, DFV, Jaranol.naringenin.6-prenylated eriodictyol, Quercetin der., Glabridin, Sigmoidin-B, licoisoflavanone, glyuranolide, 7,2’,4’-trihydroxy–5-methoxy-3–arylcoumarin, isorhamnetin, kanzonols W, Karanjin, Delphin_qt. Protein-protein interaction (PPI) network depicting the interactions of SND-related proteins involved in UC treatment.

    Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

    Techniques:

    GO and KEGG enrichment analysis of the target of OA treated by CR. ( A ) GO analysis was performed to predict biological processes/cellular components/ molecular functions affected by SND. The horizontal axis as well as the large of the dots indicate the number of small, enriched genes, the closer the colour to red means the closer the P-value is to zero, and the vertical axis indicates the name of the term. ( B ) KEGG analysis was performed to predict pathways affected by snd. The horizontal axis is the number of genes, and the vertical axis is the term name.

    Journal: Journal of Inflammation Research

    Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

    doi: 10.2147/JIR.S516556

    Figure Lengend Snippet: GO and KEGG enrichment analysis of the target of OA treated by CR. ( A ) GO analysis was performed to predict biological processes/cellular components/ molecular functions affected by SND. The horizontal axis as well as the large of the dots indicate the number of small, enriched genes, the closer the colour to red means the closer the P-value is to zero, and the vertical axis indicates the name of the term. ( B ) KEGG analysis was performed to predict pathways affected by snd. The horizontal axis is the number of genes, and the vertical axis is the term name.

    Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

    Techniques:

    Molecular docking of key components of SND and AKT1. From ( A – J ) are Q Quercetin der., Delphin_qt, licoisoflavanone, Jaranol, 6-prenylated eriodictyol, 7,2’,4’-trihydroxy–5-methoxy-3–arylcoumarin, Glabridin, kanzonols W, Sexangularetin, DFV.

    Journal: Journal of Inflammation Research

    Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

    doi: 10.2147/JIR.S516556

    Figure Lengend Snippet: Molecular docking of key components of SND and AKT1. From ( A – J ) are Q Quercetin der., Delphin_qt, licoisoflavanone, Jaranol, 6-prenylated eriodictyol, 7,2’,4’-trihydroxy–5-methoxy-3–arylcoumarin, Glabridin, kanzonols W, Sexangularetin, DFV.

    Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

    Techniques:

    Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin). A The root mean square deviation (RMSD) of AKT1-Delphin complex system, AKT1-Quercetin complex system, and AKT1-Sexangularetin complex system, the smaller the deviation, the better the conformational stability. B-C Radius of Gyration (Rg) and solvent-accessible surface area (SASA) of AKT1-Delphin, AKT1-Quercetin and AKT1-Sexangularetin composite systems, the slight fluctuation of the complex during movement indicates that the complex system has undergone conformational changes during movement. D The number of hydrogen bonds between small molecules and target proteins in the kinetic process, and the number of hydrogen bonds between AKT1-Delphin complex systems ranged from 0 to 9. In most cases, the complex has about six hydrogen bonds. The number of hydrogen bonds between the AKT1-Quercetin der complex systems ranges from 0 to 4. In most cases, the complex has about three hydrogen bonds. The number of hydrogen bonds between the AKT1-Sexangularetin complex systems ranges from 0 to 6. In most cases, the complex has about four hydrogen bonds. E Root mean square fluctuation (RMSF) of AKT1-Delphin, AKT1-Quercetin der and AKT1-Sexangularetin complex Systems.

    Journal: Journal of Inflammation Research

    Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

    doi: 10.2147/JIR.S516556

    Figure Lengend Snippet: Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin). A The root mean square deviation (RMSD) of AKT1-Delphin complex system, AKT1-Quercetin complex system, and AKT1-Sexangularetin complex system, the smaller the deviation, the better the conformational stability. B-C Radius of Gyration (Rg) and solvent-accessible surface area (SASA) of AKT1-Delphin, AKT1-Quercetin and AKT1-Sexangularetin composite systems, the slight fluctuation of the complex during movement indicates that the complex system has undergone conformational changes during movement. D The number of hydrogen bonds between small molecules and target proteins in the kinetic process, and the number of hydrogen bonds between AKT1-Delphin complex systems ranged from 0 to 9. In most cases, the complex has about six hydrogen bonds. The number of hydrogen bonds between the AKT1-Quercetin der complex systems ranges from 0 to 4. In most cases, the complex has about three hydrogen bonds. The number of hydrogen bonds between the AKT1-Sexangularetin complex systems ranges from 0 to 6. In most cases, the complex has about four hydrogen bonds. E Root mean square fluctuation (RMSF) of AKT1-Delphin, AKT1-Quercetin der and AKT1-Sexangularetin complex Systems.

    Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

    Techniques: Solvent