Related Experiment Video
Updated: Jul 13, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Protein homology detection and fold inference through multiple alignment entropy profiles.
Alejandro Sánchez-Flores1, Ernesto Pérez-Rueda, Lorenzo Segovia
1Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México.
Proteins
|August 3, 2007
Summary
This study introduces HIP, a novel method for protein homology detection using entropy profiles and pseudocodes. HIP accurately identifies relationships between proteins with similar folds, even with low sequence similarity.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Bioinformatics
Background:
- Homology detection and protein structure prediction are crucial in bioinformatics.
- Traditional sequence comparison methods struggle with low sequence similarity.
- Profile-based methods, derived from multiple sequence alignments, enhance homology detection and structure prediction.
Purpose of the Study:
- To develop and evaluate a novel method, HIP (Homology Identification with Profiles), for improved homology detection.
- To assess the impact of different amino acid classifications on profile information and recognition accuracy.
- To establish pseudocodes derived from entropy profiles as a tool for identifying distantly related protein folds.
Main Methods:
- Calculated entropy profiles from PSI-BLAST-derived multiple alignments.
- Employed various amino acid classifications (nearly 500 attributes) to generate profiles.
- Converted entropy profiles into pseudocodes for comparison using the FASTA program and an ad-hoc matrix.
- Tested performance on a nonredundant dataset with <40% sequence identity.
Main Results:
- HIP demonstrated higher accuracy in detecting relationships between proteins with similar folds compared to PSI-BLAST, COMPASS, and HHSEARCH.
- Utilizing diverse amino acid classifications significantly improved the recognition of distantly related protein folds.
- The method successfully identified relationships in proteins with less than 40% sequence identity.
Conclusions:
- Pseudocodes representing profile information offer a fast and powerful approach for homology detection and fold assignment.
- The HIP method enhances the analysis of evolutionary information within protein profiles.
- This approach improves the identification of structural features and relationships between evolutionarily distant proteins.
More Related Videos
Related Concept Videos
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...
01:25Protein Folding
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
01:22Protein Folding
Overview
01:22Protein Folding
Overview
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...
01:29Protein Folding Quality Check in the RER
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...