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Updated: Jul 4, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
A protein structure prediction service in the ProGenGrid system
Maria Mirto1, Alessandra Ferramosca, Daniele Tartarini
1SPACI Consortium, University of Salento, Lecce & NNL/CNR-INFM, Lecce, Italy. maria.mirto@unile.it
Studies in Health Technology and Informatics
|June 19, 2008
Summary
We developed a protein structure prediction service using grid computing. This service successfully predicted the dicarboxylate carrier protein structure in yeast, visualized with virtual reality.
Area of Science:
- Computational biology
- Structural bioinformatics
- Grid computing
Background:
- Protein tertiary structure prediction is crucial for understanding protein function.
- Grid computing offers a powerful platform for computationally intensive tasks like protein modeling.
- Accurate protein structure visualization aids in biological interpretation.
Purpose of the Study:
- To describe a novel protein tertiary structure prediction service.
- To implement this service within a Grid Environment.
- To predict and visualize the structure of the Saccharomyces cerevisiae dicarboxylate carrier (DIC).
Main Methods:
- Utilized a homology modeling approach for protein structure prediction.
- Implemented the service on a Grid Environment for distributed computation.
- Employed interactive virtual reality (VR) using X3D and Ajax3d technologies for model visualization.
Main Results:
- Successfully predicted the tertiary structure of the Saccharomyces cerevisiae dicarboxylate carrier.
- Demonstrated the feasibility of using a Grid Environment for protein structure prediction.
- Enabled interactive visualization of the predicted protein model in a VR environment.
Conclusions:
- The developed Grid-based service is effective for protein tertiary structure prediction.
- Homology modeling combined with VR visualization provides valuable insights into protein structures.
- This approach can be extended to predict and analyze other protein structures.
Related Concept Videos
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.
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...