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Updated: Jul 20, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.
Nandini Krishnamurthy1, Duncan P Brown, Dan Kirshner
1Department of Bioengineering, 473 Evans Hall #1762, University of California, Berkeley, CA 94720, USA.
Genome Biology
|September 16, 2006
Summary
PhyloFacts is a structural phylogenomic encyclopedia with nearly 10,000 protein family entries. It helps biologists avoid errors in protein function prediction by integrating diverse data within an evolutionary framework.
Area of Science:
- * Phylogenomics
- * Structural Biology
- * Bioinformatics
Background:
- * Protein function prediction is crucial for biological research.
- * Homology-based methods can introduce systematic errors.
- * Integrating diverse data is necessary for accurate functional analysis.
Purpose of the Study:
- * To present PhyloFacts, a comprehensive structural phylogenomic encyclopedia.
- * To provide a resource for accurate protein function prediction.
- * To enable biologists to avoid errors in functional inference.
Main Methods:
- * Development of a structural phylogenomic encyclopedia ('PhyloFacts').
- * Integration of experimental data and bioinformatics methods.
- * Application of an evolutionary framework for analysis.
Main Results:
- * PhyloFacts contains nearly 10,000 entries for protein families and domains.
- * Pre-calculated structural, functional, and evolutionary analyses are available.
- * The resource facilitates classification of user-submitted sequences.
Conclusions:
- * PhyloFacts offers a robust framework for understanding protein evolution and function.
- * The encyclopedia minimizes systematic errors in function prediction.
- * It serves as a valuable web resource for the biological community.
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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...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
01:13Protein Organization
Overview
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.