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MVP: Macromolecular Visualization and Processing

Dong Xu and Yang Zhang

Purpose:

    Sometimes, our aim is not only to see 3D molecular structures, but also to get derived computational results from the structures and visualize them simultaneously. Currently, MVP is mainly for the illustration and processing of structure-related information which is useful in structure prediction.

Downloadable Version 1.0:

Development Information:

    Language: C++, OpenGL

    GUI design: wxWidgets

    Compiler and dependence: MSVS in Windows; GCC+GTK in Linux

Highlights:

    1. Secondary strucutre estimation and visualization for alpha-carbon backbone

    During the protein tertiary structure prediction, the decoy may only contains alpha carbons. However, we still want to check out if the backbone conformation is possible to form hydrogen bond after add mainchain heavy atoms.

    2. Visualization of trajectories after Monte Carlo or molecular dynamics simulation

    3. Depth calculation and visualization

    Depth is the minimum distance to the surface. It reveals the hydrophobic property of each residue.

    per atom
    per residue

     

Basic Components:

    1. Protein tertiary structure (styles, colors)

    backbone, charge
    spacefill, CPK
    wireframe, amino type
    stick, shapely
    strands, acidity
    ribbons, structure
    cartoon, group
    ballstick, hydropathy

    2. Cryo-EM density maps

    pointcloud
    mesh
    isosurface

    3. Contact visualization

    If predicted contact is consistent with that in the native structure, then the line is solid red, else is dash blue.

    4. Principal axes

    Using Principal Component Analysis (PCA), transform the structure to the standard position.

    before PCA
    after PCA

    5. RNA and DNA visualization

     

     

     

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