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Related Concept Videos

Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Oriented Surfaces01:30

Oriented Surfaces

A surface is called orientable if a consistent choice of unit normal vector can be made at every point on the surface. A thin soap film stretched across a wire loop provides a familiar example. The film separates the air on one side from the air on the other, so one side can be selected as positive and the opposite side as negative. Once this choice is made, a unit normal vector can be assigned smoothly across the entire surface.At each point on the soap film, a unit normal vector points...
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.Two regions of electron density in a diatomic...

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3D Printing of Biomolecular Models for Research and Pedagogy
09:17

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Published on: March 13, 2017

Bio-molecule Surfaces Construction via a Higher-Order Level-Set Method.

Chandrajit L Bajaj, Guo-Liang Xu, Qin Zhang

    Journal of Computer Science and Technology
    |September 28, 2011
    PubMed
    Summary
    This summary is machine-generated.

    We developed a higher-order spline level-set (HLS) method for constructing biomolecule surfaces. This efficient computational approach accurately models implicit solvation interfaces using geometric partial differential equations.

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    Area of Science:

    • Computational Biology
    • Biophysics
    • Applied Mathematics

    Background:

    • Accurate biomolecular surface construction is crucial for understanding molecular interactions and solvation.
    • Existing methods may lack the precision or efficiency required for complex molecular systems.

    Purpose of the Study:

    • To introduce a novel higher-order spline level-set (HLS) framework.
    • To apply the HLS method for the efficient and accurate construction of biomolecular surfaces.

    Main Methods:

    • Developed a general level-set formulation of geometric partial differential equations.
    • Employed a C(2) spline basis for efficient numerical solutions.
    • Implemented a fast cubic spline interpolation algorithm leveraging convolution and Z-transform.

    Main Results:

    • Demonstrated the HLS method's capability in constructing implicit solvation interfaces for biomolecules.
    • The method utilizes atomic coordinates and solvated radii as input.
    • Achieved efficient computation through spline-based techniques.

    Conclusions:

    • The higher-order spline level-set method offers an efficient and accurate framework for biomolecular surface generation.
    • This approach advances the computational modeling of solvation phenomena in biological systems.