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Updated: Jun 1, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
State-of-the-art bioinformatics protein structure prediction tools (Review)
Athanasia Pavlopoulou1, Ioannis Michalopoulos
1Department of Pharmacy, School of Health Sciences, University of Patras, Rion-Patras, Greece.
International Journal of Molecular Medicine
|May 28, 2011
Summary
Understanding protein structure is key to function. This study offers bioinformatics tools to predict protein structures from amino acid sequences, aiding experimental biologists in their research.
Area of Science:
- * Computational Biology and Structural Bioinformatics
Background:
- * Experimental protein structure determination lags behind genomic data, creating a knowledge gap.
- * The postgenomics era presents challenges in understanding protein function due to the vast number of proteins with unknown structures.
Purpose of the Study:
- * To curate and present a set of advanced, evaluated, and user-friendly computational tools for protein structure prediction.
- * To assist experimental biologists in interpreting their findings and designing new experiments through accurate structure prediction.
Main Methods:
- * Review and evaluation of existing automated bioinformatics tools for protein structure prediction.
- * Focus on user-friendliness and accessibility for experimental biologists.
Main Results:
- * A collection of cutting-edge computational tools for protein structure prediction has been identified and evaluated.
- * The tools are designed to be user-friendly for biologists lacking deep computational expertise.
Conclusions:
- * Bioinformatics tools can bridge the gap between protein sequence and structure information.
- * Providing accessible prediction tools empowers experimental biologists to advance their research and experimental design.
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
01:24Protein 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...
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...