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Updated: Jul 10, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Pfam: a domain-centric method for analyzing proteins and proteomes
Methods in Molecular Biology (Clifton, N.J.)
|November 21, 2007
Summary
Pfam is a protein families database that helps biologists manage vast amounts of genome sequencing data. It offers tools for annotation, classification, and comparison of proteins and proteomes.
Area of Science:
- Bioinformatics
- Genomics
- Proteomics
Background:
- The increasing volume of genome sequencing data presents challenges for protein annotation and comparison.
- Efficient discovery and access to protein data are crucial for biological research.
Purpose of the Study:
- To describe the utilization of the Pfam database web interface.
- To outline the resources and tools available within Pfam for protein data analysis.
Main Methods:
- Utilizing the Pfam web interface for accessing protein family data.
- Employing Pfam's resources including sequence alignments, phylogenetic trees, and profile hidden Markov models (HMMs).
- Exploiting search tools for sequences, domain combinations, taxonomy, and proteome browsing/comparison.
Main Results:
- Detailed description of Pfam's web interface functionalities.
- Explanation of how to use Pfam's diverse resources for biological data analysis.
- Demonstration of various search and browsing capabilities within the database.
Conclusions:
- Pfam provides essential tools and resources for annotating, classifying, and comparing protein families.
- The database facilitates efficient discovery and access to proteomic information for biologists.
- Effective use of Pfam aids in managing and interpreting large-scale genomic and proteomic datasets.
Related Concept Videos
02:47Protein 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...
02:47Protein 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...
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:26Protein 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,...
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,...
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...