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Newman Projections

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.

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

Fischer Projections

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...

Molecular Shapes

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...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Molecular Shape and Polarity

Molecular Shape and Polarity

Dipole Moment of a Molecule

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Related Experiment Video

Updated: May 30, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.

Daisuke Kihara¹, Lee Sael, Rayan Chikhi

¹Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN 47907, USA. dkihara@purdue.edu

Current Protein & Peptide Science

|July 27, 2011

Summary

The 3D Zernike descriptor (3DZD) offers a rotation-invariant method for representing protein tertiary structures. This technique enables rapid comparison of molecular surfaces, facilitating efficient database screening and interaction analysis.

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Area of Science:

Structural Biology
Computational Biology
Bioinformatics

Background:

Increasing availability of protein tertiary structure data necessitates advanced computational tools.
Existing methods for protein structure comparison and interaction analysis require optimization.
Efficiently characterizing molecular surfaces is crucial for understanding protein function.

Purpose of the Study:

To introduce and review the applications of the 3D Zernike descriptor (3DZD) for protein structure analysis.
To highlight the 3DZD's capability in representing and comparing molecular surfaces.
To demonstrate the utility of 3DZD in computational screening of protein structure databases.

Main Methods:

The 3D Zernike descriptor (3DZD) represents 3D molecular surfaces as a compact vector of coefficients.
3DZD is derived from a series expansion of a mathematical 3D function.
Invariance to rotation is a key feature of the 3DZD method.

Main Results:

The 3DZD provides a compact and rotation-invariant representation of protein tertiary structures.
This representation allows for rapid comparison of surface shapes.
The method is suitable for real-time screening of large protein structure databases.

Conclusions:

The 3D Zernike descriptor is an effective computational technique for analyzing protein structures.
Its rotation invariance and compact representation enable efficient database searching and interaction studies.
The 3DZD holds significant potential for advancing structural bioinformatics and drug discovery.