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Related Concept Videos

Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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.
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...
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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 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...

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Updated: Jun 24, 2026

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 Server: automated enzyme function prediction in protein structures using 3D templates.

R Matthew Ward1, Eric Venner, Bryce Daines

  • 1Department of Molecular and Human Genetics, Program in Structural and Computational Biology and Molecular, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

Bioinformatics (Oxford, England)
|March 25, 2009
PubMed
Summary
This summary is machine-generated.

The Evolutionary Trace Annotation (ETA) Server predicts protein enzymatic activity using phylogenetic analysis and 3D template matching. This method achieves high accuracy, minimizing false predictions for structural genomics.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • The Evolutionary Trace Annotation (ETA) Server is a web application.
  • It is accessible at http://mammoth.bcm.tmc.edu/eta/.

Purpose of the Study:

  • To predict enzymatic activity of proteins with unknown functions.
  • To leverage the Evolutionary Trace (ET) method for functional residue identification.
  • To develop a 3D template for proposing protein function.

Main Methods:

  • Utilizes the phylogenetic Evolutionary Trace (ET) method to identify key functional residues from protein structures.
  • Extracts a 3D template representing the proposed function.
  • Searches annotated structures for geometric template matches indicating functional mimicry.
  • Applies specificity filters: evolutionary similarity, function plurality, and match reciprocity.

Main Results:

  • Achieves 43% prediction coverage in large-scale enzyme controls.
  • Reports a 92% positive predictive value, minimizing false annotations.
  • Enables users to modify search parameters and templates.

Conclusions:

  • The ETA Server expands the ET suite for protein structure annotation.
  • It effectively predicts enzymatic activity and proposes function-associated 3D motifs.
  • Contributes to the annotation efforts of metaservers.