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Related Concept Videos

Protein Organization01:24

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.
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Improved protein surface comparison and application to low-resolution protein structure data.

Lee Sael1, Daisuke Kihara

  • 1Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA. lee399@cs.purdue.edu

BMC Bioinformatics
|December 22, 2010
PubMed
Summary
This summary is machine-generated.

3D Zernike descriptors (3DZDs) improve protein structure comparison for bioinformatics. Representing backbone atoms with 3DZDs enhances retrieval performance, especially when combined with all-atom surfaces, aiding function prediction for unknown protein structures.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Advancements in protein structure determination present challenges for bioinformatics.
  • A large number of proteins with unknown functions require rapid functional clues.
  • Existing structure comparison methods are too slow for real-time database searches.
  • Low-resolution data from techniques like electron microscopy (EM) pose new challenges.

Purpose of the Study:

  • To evaluate new surface representations for protein structure comparison using 3D Zernike descriptors (3DZDs).
  • To assess the applicability of 3DZDs for searching low-resolution electron microscopy (EM) density maps.
  • To improve the speed and accuracy of protein function prediction for large-scale structure databases.

Main Methods:

  • Developed and examined three new surface representations: backbone atoms, all-atom surface, and a combined representation.
  • Encoded all surface representations using 3D Zernike descriptors (3DZDs) for rotation-invariant and compact data.
  • Evaluated retrieval performance using SCOP and CE-based classifications for structure retrieval.

Main Results:

  • 3D Zernike descriptors (3DZDs) representing backbone atoms showed superior retrieval performance compared to the original all-atom surface representation.
  • Combining backbone and all-atom surface representations further improved retrieval accuracy.
  • The 3D Zernike descriptor method demonstrated effectiveness in comparing low-resolution protein structures.

Conclusions:

  • 3D Zernike descriptors (3DZDs) offer a fast and effective method for protein structure comparison and function prediction.
  • Backbone atom representation combined with 3DZDs significantly enhances structure retrieval accuracy.
  • The 3D Zernike descriptor approach is robust for analyzing low-resolution structural data, including EM maps.