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Updated: Jul 14, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
Marc A Marti-Renom1, Andrea Rossi, Fátima Al-Shahrour
1Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain. mmarti@cipf.es
BMC Bioinformatics
|June 30, 2007
Summary
New tools, AnnoLite and AnnoLyze, automatically annotate protein structures using comparative analysis. These programs transfer functional annotations from known structures, addressing a key gap in structural biology research.
Area of Science:
- Structural biology
- Structural genomics
- Computational biology
Background:
- Rapid increase in experimentally determined protein structures.
- Lack of functional information for many deposited structures.
- Need for automated protein function annotation tools.
Purpose of the Study:
- Develop tools for automatic and comprehensive protein structure function annotation.
- Apply comparative protein structure annotation to transfer functional information.
- Introduce AnnoLite and AnnoLyze programs.
Main Methods:
- Utilizing structural alignments from the DBAli database.
- Employing comparative protein structure annotation.
- Developing AnnoLite for predicting functional terms and AnnoLyze for binding sites and interaction patches.
Main Results:
- AnnoLite achieves ~90% sensitivity and ~80% precision for predicting SCOP, CATH, EC, InterPro, PfamA, and GO terms.
- AnnoLyze predicts ligand binding sites and domain interaction patches with ~70% sensitivity and ~30% precision.
- AnnoLyze correctly localizes small molecule binding sites in ~95% of predictions.
Conclusions:
- AnnoLite and AnnoLyze provide reliable and automatic annotation of protein structures.
- These tools facilitate functional annotation transfer through comparative analysis.
- The programs are accessible online as part of the DBAli suite.
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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.
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
01:24Protein 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.
02:15Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
02:15Protein and Protein Structures
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...