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Related Concept Videos

Protein Families02:47

Protein 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...
Protein Families02:47

Protein 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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Updated: Jun 27, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein function predictions based on the phylogenetic profile method.

Zhenran Jiang1

  • 1Computer Science & Technology Department, East China Normal University, Shanghai, China. zrjiang@cs.ecnu.edu.cn

Critical Reviews in Biotechnology
|December 4, 2008
PubMed
Summary
This summary is machine-generated.

Phylogenetic profiles offer a promising computational strategy for predicting protein function in the post-genomics era. This review highlights progress and challenges in using comparative genomics to understand protein relationships and molecular networks.

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Last Updated: Jun 27, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

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Published on: November 3, 2011

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Inferring protein functional relationships is a key challenge in post-genomics research.
  • Comparative genomics offers powerful methods for understanding protein function.
  • Phylogenetic profiles have emerged as a valuable predictor of protein-protein interactions.

Purpose of the Study:

  • To review recent advancements in protein function prediction using the phylogenetic profile method.
  • To highlight current challenges in computational protein function prediction.
  • To emphasize the potential of comparative genomic strategies for elucidating protein functions.

Main Methods:

  • Review of literature on phylogenetic profile applications.
  • Analysis of comparative genomics approaches for protein function inference.
  • Summary of relevant bioinformatics resources.

Main Results:

  • The phylogenetic profile method is a proven strategy for inferring protein relationships.
  • Significant progress has been made in applying this method for protein function prediction.
  • Several informatics resources are available to support this research.

Conclusions:

  • Comparative genomics, particularly the phylogenetic profile method, holds great promise for predicting protein function.
  • Integration of these methods with other computational tools can provide deeper insights into molecular networks.
  • Addressing current challenges is crucial for advancing protein function prediction.