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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...
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-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...
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,...

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Related Experiment Video

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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

Identifying protein domains with the Pfam database.

Penny Coggill1, Robert D Finn1, Alex Bateman1

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

Current Protocols in Bioinformatics
|September 27, 2008
PubMed
Summary

Pfam is a comprehensive protein domain database. This guide explains how to access and use its protein families, alignments, and annotation data, both online and locally.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Genomics

Background:

  • Protein domains are fundamental units of proteins, crucial for function and evolution.
  • Databases like Pfam organize and provide access to these protein domains.
  • Understanding protein domain families aids in functional prediction and evolutionary analysis.

Purpose of the Study:

  • To provide a detailed guide on accessing and utilizing the Pfam database.
  • To explain how to retrieve and interpret protein families, multiple sequence alignments, and associated annotations.
  • To instruct users on running Pfam tools both remotely and locally.

Main Methods:

  • Accessing Pfam via the World Wide Web and flatfile formats.
  • Utilizing multiple sequence alignments and profile hidden Markov models (HMMs).
  • Leveraging associated annotation and cross-database links for comprehensive analysis.

Main Results:

  • Pfam entries are readily available, offering extensive information on protein domain families.
  • Users can effectively access and interpret protein family data, including alignments and annotations.
  • The guide facilitates both remote and local execution of Pfam tools.

Conclusions:

  • Pfam serves as an essential resource for protein domain family information.
  • Effective utilization of Pfam enhances protein function prediction and research.
  • The database and its associated tools are accessible for diverse bioinformatics applications.