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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...
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.
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,...
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...

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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

Protein function annotation by homology-based inference.

Yaniv Loewenstein1, Domenico Raimondo, Oliver C Redfern

  • 1Department of Biological Chemistry, The Hebrew University of Jerusalem, Sudarsky Center, Jerusalem 91904, Israel.

Genome Biology
|February 20, 2009
PubMed
Summary
This summary is machine-generated.

Computational tools are vital for analyzing sequenced genomes. This review covers automated protein function prediction using sequence and structure data.

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • The increasing volume of sequenced genomes necessitates advanced computational methods for gene and protein characterization.
  • Accurate annotation of genomic data is crucial for understanding biological functions and pathways.

Purpose of the Study:

  • To review the progress in automated protein function prediction.
  • To highlight tools developed by the BioSapiens Network for genome annotation.

Main Methods:

  • Review of computational annotation tools.
  • Analysis of protein sequence and structure data for function prediction.

Main Results:

  • The BioSapiens Network has developed comprehensive tools for genome annotation.
  • Significant advancements have been made in automated protein function prediction.

Conclusions:

  • Automated prediction of protein function is a key area in bioinformatics.
  • Sequence and structure-based methods are essential for characterizing proteins from genomic data.