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Related Concept Videos

Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Conservation of Protein Domains Over Different Proteins02:26

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...
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.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Multi-view methods for protein structure comparison using latent dirichlet allocation.

S Shivashankar1, S Srivathsan, B Ravindran

  • 1Department of Computer Science and Engineering, IIT Madras, Chennai-600 036.

Bioinformatics (Oxford, England)
|June 21, 2011
PubMed
Summary

This study introduces an improved protein structure representation using a topic model for efficient retrieval of similar protein structures. The novel multi-viewpoint framework enhances the identification of both close and remote protein homologs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Efficient retrieval of similar protein structures from expanding databases is crucial.
  • Existing methods like the bag of fragments (FragBag) model offer basic information retrieval capabilities.
  • Key challenges include effective protein structure representation and diverse retrieval framework development.

Purpose of the Study:

  • To propose an improved protein structure representation using latent Dirichlet allocation (LDA) topic models.
  • To develop a multi-viewpoint framework for diverse protein structure retrieval, including close and remote homologs.
  • To evaluate the proposed methods against state-of-the-art techniques on a benchmark dataset.

Main Methods:

  • Utilized latent Dirichlet allocation (LDA) topic modeling for enhanced protein structure representation.
  • Developed a multi-viewpoint retrieval framework integrating multiple representations and techniques.
  • Compared performance on a benchmark dataset from Kolodny et al.

Main Results:

  • The proposed LDA-based representation significantly improves protein structure comparison.
  • The multi-viewpoint framework effectively addresses diverse retrieval needs, including homolog identification.
  • The novel techniques demonstrated superior performance compared to existing state-of-the-art methods.

Conclusions:

  • The LDA topic model offers a powerful approach for protein structure representation.
  • The multi-viewpoint framework enhances the accuracy and scope of protein structure retrieval.
  • This work advances the field of bioinformatics by providing more efficient and effective tools for analyzing protein structure data.