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Related Concept Videos

Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...

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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

Evolutionary trace annotation of protein function in the structural proteome.

Serkan Erdin1, R Matthew Ward, Eric Venner

  • 1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. serdin@bcm.tmc.edu

Journal of Molecular Biology
|December 29, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces Evolutionary Trace Annotation (ETA), a method using 3D structural templates of critical residues to predict protein functions. ETA successfully annotates proteins lacking homology, aiding structural genomics research.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Structural genomics (SG) produces many protein structures lacking clear functional annotations.
  • Homology-based function prediction is insufficient for novel or uncharacterized proteins.
  • Predicting protein function is crucial for understanding biological processes.

Purpose of the Study:

  • To develop and evaluate a novel method for protein function prediction using 3D structural templates.
  • To leverage Evolutionary Trace (ET) rankings to identify functionally critical residues for template construction.
  • To assign Gene Ontology (GO) functions to proteins, including enzymes and non-enzymes, from structural data.

Main Methods:

  • Constructing 3D templates from evolutionarily conserved residues identified by ET rankings.
  • Matching these 3D templates against protein structures.
  • Assigning GO functions based on template matches.
  • Evaluating prediction accuracy in high-specificity and high-sensitivity modes.

Main Results:

  • The Evolutionary Trace Annotation (ETA) method achieved 53% coverage in high-specificity mode with 84% all-depth positive predictive value (PPV).
  • High-sensitivity mode increased coverage to 84% with a 75% all-depth PPV.
  • ETA successfully predicted functions in 42% of unannotated SG proteins, with high expected accuracy.

Conclusions:

  • Local structural comparisons of evolutionarily important residues are effective for deciphering protein functions.
  • ETA provides reliable function predictions without prior assumptions on mechanisms.
  • The method aids in annotating proteins from structural genomics efforts.