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software for visual interactive analysis of molecular dynamics  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc software for visual interactive analysis of molecular dynamics
    Software For Visual Interactive Analysis Of Molecular Dynamics, 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/interactive+visualization+software/visual+molecular+dynamics+program/pm39976539-327-16-20
    Average 90 stars, based on 1 article reviews
    software for visual interactive analysis of molecular dynamics - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Derivative Assay:

    Article Title: Internal Cavity versus External Cavity: A Theoretical Study of Molecular Recognition of Biphenarene.
    Article Snippet: Crystalline macrocyclic materials hold great promise for the efficient separation of compounds with similar structures and properties via selective molecular recognition.. Notably, the crystal packing of the macrocycles creates new intermolecular external cavities capable of accommodating guest molecules in a manner distinct from molecular recognition in solution, thereby exhibiting different adsorption properties.. This work focuses on the guest recognition mechanisms of MeBP3, a new type of macrocyclic arene, in a crystal environment.

    Article Title: Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations.
    Article Snippet: The MscL structures were rendered using the Visual Molecular Dynamics (VMD) program.39 We started with 12 replicas of the MscL mutant and equilibrated them at zero surface tension for 200 ns (the workflow of a single replica simulation is illustrated in Figure 2a).

    Article Title: On the Engulfment of Antifreeze Proteins by Ice
    Article Snippet: The snapshots were visualized using the Visual Molecular Dynamics (VMD) package (11).

    Article Title: Stability of colloidal gas aphrons based on polymer-surfactant formulations and molecular dynamics insights
    Article Snippet: To visualize and study the simulation results Visual Molecular Dynamics (VMD) tool was used .

    Article Title: Cooperative Role of Mixed Solvent in the Evaporation-Induced Self-Assembly of Polypeptoid Nanocrystals
    Article Snippet: The simulated structures were visualized using the Visual Molecular Dynamics (VMD) package.

    Article Title: An Electrochromic Pure Poly( N -phenylglycine) with a High Optical Modulation Amplitude, a Wide Color Gamut, and Safe Raw Material Accessibility.
    Article Snippet: Conductive polymer-based electrochromic materials (ECMs), distinguished by their wide color tunability and low cost, are limited particularly in terms of their optical modulation range and response time; meanwhile, their monomers pose significant risks to human health and the environment.. In this work, we report a nontoxic polyaniline (PANI)-based derivative, poly(N-phenylglycine) (PNPG).. By introducing carboxyl groups onto the nitrogen atoms of the polymer backbone, the conjugated and electronic structure of the polymer was modified, thus reducing the bandgap of PNPG and facilitating charge transportation.

    Article Title: Oscillations in incident electric field enhances interfacial water evaporation.
    Article Snippet: Visualization is performed in perspective display mode using the Visual Molecular Dynamics (VMD) package.44 (b) Water density profile along y-direction for both cases, i.e., with and without hydrogel.

    Software:

    Article Title: Internal Cavity versus External Cavity: A Theoretical Study of Molecular Recognition of Biphenarene.
    Article Snippet: Crystalline macrocyclic materials hold great promise for the efficient separation of compounds with similar structures and properties via selective molecular recognition.. Notably, the crystal packing of the macrocycles creates new intermolecular external cavities capable of accommodating guest molecules in a manner distinct from molecular recognition in solution, thereby exhibiting different adsorption properties.. This work focuses on the guest recognition mechanisms of MeBP3, a new type of macrocyclic arene, in a crystal environment.

    Article Title: Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations.
    Article Snippet: The MscL structures were rendered using the Visual Molecular Dynamics (VMD) program.39 We started with 12 replicas of the MscL mutant and equilibrated them at zero surface tension for 200 ns (the workflow of a single replica simulation is illustrated in Figure 2a).

    Article Title: On the Engulfment of Antifreeze Proteins by Ice
    Article Snippet: The snapshots were visualized using the Visual Molecular Dynamics (VMD) package (11).

    Article Title: Stability of colloidal gas aphrons based on polymer-surfactant formulations and molecular dynamics insights
    Article Snippet: To visualize and study the simulation results Visual Molecular Dynamics (VMD) tool was used .

    Article Title: Cooperative Role of Mixed Solvent in the Evaporation-Induced Self-Assembly of Polypeptoid Nanocrystals
    Article Snippet: The simulated structures were visualized using the Visual Molecular Dynamics (VMD) package.

    Article Title: An Electrochromic Pure Poly( N -phenylglycine) with a High Optical Modulation Amplitude, a Wide Color Gamut, and Safe Raw Material Accessibility.
    Article Snippet: Conductive polymer-based electrochromic materials (ECMs), distinguished by their wide color tunability and low cost, are limited particularly in terms of their optical modulation range and response time; meanwhile, their monomers pose significant risks to human health and the environment.. In this work, we report a nontoxic polyaniline (PANI)-based derivative, poly(N-phenylglycine) (PNPG).. By introducing carboxyl groups onto the nitrogen atoms of the polymer backbone, the conjugated and electronic structure of the polymer was modified, thus reducing the bandgap of PNPG and facilitating charge transportation.

    Article Title: Oscillations in incident electric field enhances interfacial water evaporation.
    Article Snippet: Visualization is performed in perspective display mode using the Visual Molecular Dynamics (VMD) package.44 (b) Water density profile along y-direction for both cases, i.e., with and without hydrogel.



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    ( A ) <t>3D</t> surface projection of IHCs and OHCs from the cochlear 32 kHz region of Clic5 +/− , Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red) and actin (gray). ( B ) Representative confocal images of IHCs from the apical turn of Clic5 +/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red), actin (gray), and FLAG tag (green). ( C ) Representative confocal images of IHCs and OHCs from the cochlear 8 kHz region of Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with actin. ( D ) Stereocilia length measurements of IHC at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( E ) Quantification of OHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( F ) Quantification of IHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( G ) High-magnification scanning electron <t>microscopy</t> images of outer and inner hair bundles from the cochlea middle-turn of the Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks. ( H ) Representative images of IHCs and OHCs at 12 weeks at different regions of the cochlea of Clic5 −/ − injected with scAAV. Clic5 . ( I ) ABR thresholds at 4 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( J ) ABR thresholds at 8 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 11), and Clic5 −/− injected with scAVV. Clic5 (n = 7). ( K ) ABR thresholds at 12 weeks of Clic5 +/− ( n = 10), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 7). ( L ) DPOAE thresholds at 4 weeks of Clic5 +/− ( n = 12), Clic5 −/ − ( n = 12), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( M ) ABR thresholds at 3-time points of Clic5 −/− injected with scAAV. Clic5: 4 weeks ( n = 10), 8 weeks ( n = 7), and 12 weeks ( n = 7). ( N ) Freezing behavior duration in a fear conditioning assay at 12 weeks of Clic5 +/− ( n = 14), Clic5 − /− ( n = 14), and Clic5 −/− injected with scAAV. Clic5 ( n = 6). ( O ) Expression rates of scAAV. Clic5 across the cochlea as a function of viral titer, n = 3 for each group. ( P ) ABR thresholds at 4 weeks of Clic5 −/ − injected with scAAV .Clic5 at different viral doses: 1.52 × 10¹³ gc/ml ( n = 10), 1.52 × 10 12 gc/ml ( n = 3) and 1.52 × 10 11 gc/ml ( n = 3). Data information: Statistical tests were two-way ANOVA with Holm–Sidak correction for multiple comparisons for ( D – F , I – N , P ), and one-way ANOVA followed by Tukey correction for multiple comparisons for ( O ). Plots show mean ± SD. ns not significant, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001 (Exact P values are provided in Appendix Table S ). Scale bars = 10 μm for ( A , C , H ), 2 μm for ( B ), 0.5 μm for OHC ( G ), and 2 μm for IHC ( G ). .
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    ( A ) <t>3D</t> surface projection of IHCs and OHCs from the cochlear 32 kHz region of Clic5 +/− , Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red) and actin (gray). ( B ) Representative confocal images of IHCs from the apical turn of Clic5 +/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red), actin (gray), and FLAG tag (green). ( C ) Representative confocal images of IHCs and OHCs from the cochlear 8 kHz region of Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with actin. ( D ) Stereocilia length measurements of IHC at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( E ) Quantification of OHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( F ) Quantification of IHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( G ) High-magnification scanning electron <t>microscopy</t> images of outer and inner hair bundles from the cochlea middle-turn of the Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks. ( H ) Representative images of IHCs and OHCs at 12 weeks at different regions of the cochlea of Clic5 −/ − injected with scAAV. Clic5 . ( I ) ABR thresholds at 4 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( J ) ABR thresholds at 8 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 11), and Clic5 −/− injected with scAVV. Clic5 (n = 7). ( K ) ABR thresholds at 12 weeks of Clic5 +/− ( n = 10), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 7). ( L ) DPOAE thresholds at 4 weeks of Clic5 +/− ( n = 12), Clic5 −/ − ( n = 12), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( M ) ABR thresholds at 3-time points of Clic5 −/− injected with scAAV. Clic5: 4 weeks ( n = 10), 8 weeks ( n = 7), and 12 weeks ( n = 7). ( N ) Freezing behavior duration in a fear conditioning assay at 12 weeks of Clic5 +/− ( n = 14), Clic5 − /− ( n = 14), and Clic5 −/− injected with scAAV. Clic5 ( n = 6). ( O ) Expression rates of scAAV. Clic5 across the cochlea as a function of viral titer, n = 3 for each group. ( P ) ABR thresholds at 4 weeks of Clic5 −/ − injected with scAAV .Clic5 at different viral doses: 1.52 × 10¹³ gc/ml ( n = 10), 1.52 × 10 12 gc/ml ( n = 3) and 1.52 × 10 11 gc/ml ( n = 3). Data information: Statistical tests were two-way ANOVA with Holm–Sidak correction for multiple comparisons for ( D – F , I – N , P ), and one-way ANOVA followed by Tukey correction for multiple comparisons for ( O ). Plots show mean ± SD. ns not significant, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001 (Exact P values are provided in Appendix Table S ). Scale bars = 10 μm for ( A , C , H ), 2 μm for ( B ), 0.5 μm for OHC ( G ), and 2 μm for IHC ( G ). .
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    Image Search Results


    ( A ) 3D surface projection of IHCs and OHCs from the cochlear 32 kHz region of Clic5 +/− , Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red) and actin (gray). ( B ) Representative confocal images of IHCs from the apical turn of Clic5 +/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red), actin (gray), and FLAG tag (green). ( C ) Representative confocal images of IHCs and OHCs from the cochlear 8 kHz region of Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with actin. ( D ) Stereocilia length measurements of IHC at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( E ) Quantification of OHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( F ) Quantification of IHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( G ) High-magnification scanning electron microscopy images of outer and inner hair bundles from the cochlea middle-turn of the Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks. ( H ) Representative images of IHCs and OHCs at 12 weeks at different regions of the cochlea of Clic5 −/ − injected with scAAV. Clic5 . ( I ) ABR thresholds at 4 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( J ) ABR thresholds at 8 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 11), and Clic5 −/− injected with scAVV. Clic5 (n = 7). ( K ) ABR thresholds at 12 weeks of Clic5 +/− ( n = 10), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 7). ( L ) DPOAE thresholds at 4 weeks of Clic5 +/− ( n = 12), Clic5 −/ − ( n = 12), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( M ) ABR thresholds at 3-time points of Clic5 −/− injected with scAAV. Clic5: 4 weeks ( n = 10), 8 weeks ( n = 7), and 12 weeks ( n = 7). ( N ) Freezing behavior duration in a fear conditioning assay at 12 weeks of Clic5 +/− ( n = 14), Clic5 − /− ( n = 14), and Clic5 −/− injected with scAAV. Clic5 ( n = 6). ( O ) Expression rates of scAAV. Clic5 across the cochlea as a function of viral titer, n = 3 for each group. ( P ) ABR thresholds at 4 weeks of Clic5 −/ − injected with scAAV .Clic5 at different viral doses: 1.52 × 10¹³ gc/ml ( n = 10), 1.52 × 10 12 gc/ml ( n = 3) and 1.52 × 10 11 gc/ml ( n = 3). Data information: Statistical tests were two-way ANOVA with Holm–Sidak correction for multiple comparisons for ( D – F , I – N , P ), and one-way ANOVA followed by Tukey correction for multiple comparisons for ( O ). Plots show mean ± SD. ns not significant, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001 (Exact P values are provided in Appendix Table S ). Scale bars = 10 μm for ( A , C , H ), 2 μm for ( B ), 0.5 μm for OHC ( G ), and 2 μm for IHC ( G ). .

    Journal: EMBO Molecular Medicine

    Article Title: AAV gene therapy rescues hearing and balance in a model of CLIC5 deafness

    doi: 10.1038/s44321-025-00275-7

    Figure Lengend Snippet: ( A ) 3D surface projection of IHCs and OHCs from the cochlear 32 kHz region of Clic5 +/− , Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red) and actin (gray). ( B ) Representative confocal images of IHCs from the apical turn of Clic5 +/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with a CLIC5 (red), actin (gray), and FLAG tag (green). ( C ) Representative confocal images of IHCs and OHCs from the cochlear 8 kHz region of Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 at 12 weeks, stained with actin. ( D ) Stereocilia length measurements of IHC at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( E ) Quantification of OHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( F ) Quantification of IHC survival at different regions of the cochlea, n = 3 for Clic5 +/− , Clic5 −/− , and Clic5 −/− injected with scAAV. Clic5 . ( G ) High-magnification scanning electron microscopy images of outer and inner hair bundles from the cochlea middle-turn of the Clic5 −/− and Clic5 −/− injected with scAAV. Clic5 at 12 weeks. ( H ) Representative images of IHCs and OHCs at 12 weeks at different regions of the cochlea of Clic5 −/ − injected with scAAV. Clic5 . ( I ) ABR thresholds at 4 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( J ) ABR thresholds at 8 weeks of Clic5 +/− ( n = 11), Clic5 −/− ( n = 11), and Clic5 −/− injected with scAVV. Clic5 (n = 7). ( K ) ABR thresholds at 12 weeks of Clic5 +/− ( n = 10), Clic5 −/− ( n = 10), and Clic5 −/− injected with scAAV. Clic5 ( n = 7). ( L ) DPOAE thresholds at 4 weeks of Clic5 +/− ( n = 12), Clic5 −/ − ( n = 12), and Clic5 −/− injected with scAAV. Clic5 ( n = 10). ( M ) ABR thresholds at 3-time points of Clic5 −/− injected with scAAV. Clic5: 4 weeks ( n = 10), 8 weeks ( n = 7), and 12 weeks ( n = 7). ( N ) Freezing behavior duration in a fear conditioning assay at 12 weeks of Clic5 +/− ( n = 14), Clic5 − /− ( n = 14), and Clic5 −/− injected with scAAV. Clic5 ( n = 6). ( O ) Expression rates of scAAV. Clic5 across the cochlea as a function of viral titer, n = 3 for each group. ( P ) ABR thresholds at 4 weeks of Clic5 −/ − injected with scAAV .Clic5 at different viral doses: 1.52 × 10¹³ gc/ml ( n = 10), 1.52 × 10 12 gc/ml ( n = 3) and 1.52 × 10 11 gc/ml ( n = 3). Data information: Statistical tests were two-way ANOVA with Holm–Sidak correction for multiple comparisons for ( D – F , I – N , P ), and one-way ANOVA followed by Tukey correction for multiple comparisons for ( O ). Plots show mean ± SD. ns not significant, * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001 (Exact P values are provided in Appendix Table S ). Scale bars = 10 μm for ( A , C , H ), 2 μm for ( B ), 0.5 μm for OHC ( G ), and 2 μm for IHC ( G ). .

    Article Snippet: Imaris 3D Interactive Microscopy Visualization software , Oxford Instruments . , version 10.1.

    Techniques: Injection, Staining, FLAG-tag, Electron Microscopy, Expressing