Related Experiment Video
Updated: May 5, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Pfam: the protein families database
Robert D Finn1, Alex Bateman, Jody Clements
1HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 (Viikinkaari 5), 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden.
The Pfam database now includes 1182 new protein families, maintaining nearly 80% coverage of the UniProt Knowledgebase. Recent updates enhance features and introduce new tools for computational biology research.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- Pfam is a widely utilized database of protein families, essential for genomic and proteomic research.
- The database has undergone significant expansion and feature refinement since its last major update.
Purpose of the Study:
- To detail recent updates and improvements to the Pfam database, version 27.0.
- To enhance the utility and accessibility of protein family data for the scientific community.
Main Methods:
- Comprehensive review of existing Pfam features, assessing relevance, computational load, and usage.
- Development of new features and enhancement of existing ones based on review findings.
- Inclusion of family alignments from four distinct representative proteome datasets.
Main Results:
- Addition of 1182 new protein families, bringing the total to 14,831 manually curated entries.
- Maintenance of nearly 80% sequence coverage of the UniProt Knowledgebase, despite database growth.
- Introduction of a new interactive DNA search interface and enhanced family alignments.
Conclusions:
- Pfam continues to evolve, offering improved functionality and expanded content to meet the demands of modern computational biology.
- The updated database facilitates deeper insights into protein families and their relationship with 3D structures.
Related Concept Videos
Protein Families
Protein Families
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Families
Protein Networks
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 Networks

