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simulation interactions diagram module in desmond 2018-4  (GraphPad Software Inc)


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    Structured Review

    GraphPad Software Inc simulation interactions diagram module in desmond 2018-4
    2D <t>interactions</t> <t>diagram</t> of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization <t>module</t> in Maestro 2021.4 [ , ].
    Simulation Interactions Diagram Module In Desmond 2018 4, supplied by GraphPad Software 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/result/simulation interactions diagram module in desmond 2018-4/product/GraphPad Software Inc
    Average 90 stars, based on 1 article reviews
    simulation interactions diagram module in desmond 2018-4 - by Bioz Stars, 2026-05
    90/100 stars

    Images

    1) Product Images from "Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit"

    Article Title: Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit

    Journal: Molecules

    doi: 10.3390/molecules28104108

    2D interactions diagram of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization module in Maestro 2021.4 [ , ].
    Figure Legend Snippet: 2D interactions diagram of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization module in Maestro 2021.4 [ , ].

    Techniques Used: Residue, Generated

    Averaged triplicate GluN1 LBD-ligand interactions of the 1 µs simulations. Note that figure scales are different to improve the visibility of the data. Hydrogen bonds are defined as an H-Acceptor distance less than 2.8 Å and a Donor-H-Acceptor angle greater than 120. Hydrophobic interactions include pi-pi stacking, pi-cation interactions, and van der Waals interactions within 3.6 Å of ligand. Ionic interactions are defined as charged interactions within 3.6 Å of the ligand. Water bridges are defined as H-Acceptor distances less than 2.7 Å. Hydrogen bonds are shown in green, hydrophobic interactions are shown in lilac, ionic interactions are shown in magenta, and water bridges are shown in blue. For residues with more than one type of interaction, the interaction fraction can exceed 1. ( A ) Glycine bound to wild-type GluN1 LBD, ( B ) D-serine bound to wild-type GluN1 LBD, ( C ) Glycine bound to S688Y GluN1 LBD, ( D ) D-serine bound to S688Y GluN1 LBD. Graphs were generated using the Simulation Interactions Diagram module of Maestro 2021.4 [ , ].
    Figure Legend Snippet: Averaged triplicate GluN1 LBD-ligand interactions of the 1 µs simulations. Note that figure scales are different to improve the visibility of the data. Hydrogen bonds are defined as an H-Acceptor distance less than 2.8 Å and a Donor-H-Acceptor angle greater than 120. Hydrophobic interactions include pi-pi stacking, pi-cation interactions, and van der Waals interactions within 3.6 Å of ligand. Ionic interactions are defined as charged interactions within 3.6 Å of the ligand. Water bridges are defined as H-Acceptor distances less than 2.7 Å. Hydrogen bonds are shown in green, hydrophobic interactions are shown in lilac, ionic interactions are shown in magenta, and water bridges are shown in blue. For residues with more than one type of interaction, the interaction fraction can exceed 1. ( A ) Glycine bound to wild-type GluN1 LBD, ( B ) D-serine bound to wild-type GluN1 LBD, ( C ) Glycine bound to S688Y GluN1 LBD, ( D ) D-serine bound to S688Y GluN1 LBD. Graphs were generated using the Simulation Interactions Diagram module of Maestro 2021.4 [ , ].

    Techniques Used: Generated



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    simulation interactions diagram module in desmond 2018-4  (GraphPad Software Inc)
    90
    GraphPad Software Inc simulation interactions diagram module in desmond 2018-4
    2D <t>interactions</t> <t>diagram</t> of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization <t>module</t> in Maestro 2021.4 [ , ].
    Simulation Interactions Diagram Module In Desmond 2018 4, supplied by GraphPad Software 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/result/simulation interactions diagram module in desmond 2018-4/product/GraphPad Software Inc
    Average 90 stars, based on 1 article reviews
    simulation interactions diagram module in desmond 2018-4 - by Bioz Stars, 2026-05
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    2D interactions diagram of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization module in Maestro 2021.4 [ , ].

    Journal: Molecules

    Article Title: Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit

    doi: 10.3390/molecules28104108

    Figure Lengend Snippet: 2D interactions diagram of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization module in Maestro 2021.4 [ , ].

    Article Snippet: Graphs were generated using the Simulation Interactions Diagram module in Desmond 2018-4 [ , ] and GraphPad Prism version 9.5.0 for MacOS, GraphPad Software, San Diego, CA, USA.

    Techniques: Residue, Generated

    Averaged triplicate GluN1 LBD-ligand interactions of the 1 µs simulations. Note that figure scales are different to improve the visibility of the data. Hydrogen bonds are defined as an H-Acceptor distance less than 2.8 Å and a Donor-H-Acceptor angle greater than 120. Hydrophobic interactions include pi-pi stacking, pi-cation interactions, and van der Waals interactions within 3.6 Å of ligand. Ionic interactions are defined as charged interactions within 3.6 Å of the ligand. Water bridges are defined as H-Acceptor distances less than 2.7 Å. Hydrogen bonds are shown in green, hydrophobic interactions are shown in lilac, ionic interactions are shown in magenta, and water bridges are shown in blue. For residues with more than one type of interaction, the interaction fraction can exceed 1. ( A ) Glycine bound to wild-type GluN1 LBD, ( B ) D-serine bound to wild-type GluN1 LBD, ( C ) Glycine bound to S688Y GluN1 LBD, ( D ) D-serine bound to S688Y GluN1 LBD. Graphs were generated using the Simulation Interactions Diagram module of Maestro 2021.4 [ , ].

    Journal: Molecules

    Article Title: Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit

    doi: 10.3390/molecules28104108

    Figure Lengend Snippet: Averaged triplicate GluN1 LBD-ligand interactions of the 1 µs simulations. Note that figure scales are different to improve the visibility of the data. Hydrogen bonds are defined as an H-Acceptor distance less than 2.8 Å and a Donor-H-Acceptor angle greater than 120. Hydrophobic interactions include pi-pi stacking, pi-cation interactions, and van der Waals interactions within 3.6 Å of ligand. Ionic interactions are defined as charged interactions within 3.6 Å of the ligand. Water bridges are defined as H-Acceptor distances less than 2.7 Å. Hydrogen bonds are shown in green, hydrophobic interactions are shown in lilac, ionic interactions are shown in magenta, and water bridges are shown in blue. For residues with more than one type of interaction, the interaction fraction can exceed 1. ( A ) Glycine bound to wild-type GluN1 LBD, ( B ) D-serine bound to wild-type GluN1 LBD, ( C ) Glycine bound to S688Y GluN1 LBD, ( D ) D-serine bound to S688Y GluN1 LBD. Graphs were generated using the Simulation Interactions Diagram module of Maestro 2021.4 [ , ].

    Article Snippet: Graphs were generated using the Simulation Interactions Diagram module in Desmond 2018-4 [ , ] and GraphPad Prism version 9.5.0 for MacOS, GraphPad Software, San Diego, CA, USA.

    Techniques: Generated