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Updated: Jun 2, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Improvement of protein structure comparison using a structural alphabet
Agnel Praveen Joseph1, N Srinivasan, Alexandre G de Brevern
1INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, 6, rue Alexandre Cabanel, 75739 Paris Cedex 15, France. agnel.praveen@univ-paris-diderot.fr
Biochimie
|May 17, 2011
Summary
We improved protein structure alignment using an enhanced Protein Block Alignment (iPBA) method. This method refines substitution matrices and dynamic programming for higher efficiency and accuracy in comparing protein structures.
Area of Science:
- Structural biology
- Bioinformatics
- Computational biology
Background:
- Protein three-dimensional structure is crucial for function and evolutionary studies.
- Structural alphabets, like Protein Blocks (PBs), represent local protein conformations as 1D sequences.
- Previous work utilized PBs for protein structure comparison via sequence alignment.
Purpose of the Study:
- To refine substitution matrices (SMs) and enhance the Protein Block Alignment (PBA) methodology.
- To improve the efficiency and quality of protein structure alignment.
- To develop a more effective method for mining and comparing protein structures.
Main Methods:
- Refinement of Protein Block Substitution Matrices (SMs) based on sequence and structural similarity.
- Development of an improved Protein Block Alignment (iPBA) methodology.
- Implementation of a dynamic programming algorithm that weighs local structural similarities and incorporates amino acid substitution scores.
Main Results:
- The iPBA method achieved a 6.8% increase in mining efficiency.
- Over 82% of alignments generated by iPBA showed improved quality.
- iPBA demonstrated superior performance compared to DALI and MUSTANG in 81.3% of cases, particularly for multi-domain proteins.
Conclusions:
- The enhanced Protein Block Alignment (iPBA) methodology significantly improves protein structural alignment quality and efficiency.
- iPBA offers a more accurate and effective approach for comparing protein structures, aiding functional and evolutionary analyses.
- This advancement provides a powerful tool for structural bioinformatics and drug discovery efforts.
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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.
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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.
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02:26Conservation of Protein Domains Over Different Proteins
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