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Related Concept Videos

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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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-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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Related Experiment Video

Updated: Jun 23, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

Yana Bromberg1, Guy Yachdav, Yanay Ofran

  • 1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. bromberg@rostlab.org

Current Opinion in Drug Discovery & Development
|April 28, 2009
PubMed
Summary

Automated protein function prediction is crucial for annotating vast sequence data. Novel methods like binding site prediction and in silico mutagenesis, alongside web software, promise to bridge the annotation gap.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The exponential growth of protein sequence data outpaces annotation efforts.
  • Current methods like comparative modeling and homology-based inference incompletely annotate the proteome.
  • Expert curation cannot meet the demand for comprehensive protein annotations.

Purpose of the Study:

  • To review novel automated methods for protein function prediction.
  • To explore the potential of modern web software in protein annotation.
  • To address the challenge of annotating protein sequences lacking homology.

Main Methods:

  • Discussion of automated protein function prediction through binding site and functional hotspot identification.
  • Description of comprehensive in silico mutagenesis for novel function prediction.
  • Exploration of web software for integrating 'Deep Web' data resources.

Main Results:

  • Binding site and functional hotspot predictions represent successful automated function prediction strategies.
  • Comprehensive in silico mutagenesis offers novel functional predictions and prepares for future sequencing advancements.
  • Web software integration with proprietary data can significantly enhance annotation accessibility.

Conclusions:

  • Automated protein function prediction is essential to close the annotation gap.
  • Emerging computational tools and web technologies are revolutionizing protein sequence annotation.
  • Enhanced data accessibility through web software may profoundly impact drug discovery and development.