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Related Concept Videos

Conserved Binding Sites01:49

Conserved 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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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Conservation of Protein Domains Over Different Proteins02:26

Conservation 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...
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...

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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

On position-specific scoring matrix for protein function prediction.

Jong Cheol Jeong1, Xiaotong Lin, Xue-Wen Chen

  • 1Electrical Engineering and Computer Science Department, University of Kansas, Lawrence, KS 66045, USA. jcjeong@ittc.ku.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|September 22, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces new computational methods for predicting protein functions using sequence data. These position-specific scoring matrix features improve automated genome-wide functional annotation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Vast amounts of protein sequence data are available from genome sequencing projects.
  • A significant portion of genomic data remains unannotated, hindering functional understanding.
  • Experimental methods for protein function identification are resource-intensive and time-consuming.

Purpose of the Study:

  • To develop efficient in silico methods for genome-wide functional annotation.
  • To propose novel features derived solely from protein sequences for computational function prediction.
  • To evaluate the effectiveness of these new features in predicting protein functions.

Main Methods:

  • Extraction of novel features from protein sequences using a position-specific scoring matrix.
  • Application of machine learning-based methods for computational function prediction.
  • Evaluation of feature performance using four distinct classifiers on yeast protein data.

Main Results:

  • Features derived from the position-specific scoring matrix demonstrate significant potential for bioinformatics tasks.
  • Experimental results confirm the suitability of these features for automatic function annotation.
  • The proposed in silico approach offers a practical alternative to experimental methods for large-scale annotation.

Conclusions:

  • The developed features are effective for computational protein function prediction.
  • Position-specific scoring matrix features are valuable for automated genome-wide functional annotation.
  • This work contributes to advancing in silico functional genomics and annotation strategies.