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Related Concept Videos

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...
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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein 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.
Protein Organization01:24

Protein 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.

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Related Experiment Video

Updated: Jul 3, 2026

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

A computational strategy for protein function assignment which addresses the multidomain problem.

A J Pérez1, A Rodríguez, O Trelles

  • 1Genetics Department, University of Málaga, Málaga 29071, Spain. antoniojperez@uma.es

Comparative and Functional Genomics
|July 17, 2008
PubMed
Summary
This summary is machine-generated.

This study presents a novel method for protein function assignment by correlating sequence signals with functional annotations. Utilizing feature (FT) information alongside keywords (KW) significantly improves the accuracy of function prediction, especially for sequences lacking known homologs.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Jul 3, 2026

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

Published on: January 26, 2024

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

A Protocol for Computer-Based Protein Structure and Function Prediction

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • Protein function prediction is crucial for understanding biological systems.
  • Existing methods often rely solely on sequence similarity or keyword annotations.
  • Accurate functional annotation is essential for various biological and medical applications.

Purpose of the Study:

  • To develop and evaluate a novel method for assigning functions to unknown protein sequences.
  • To investigate the utility of incorporating positional feature (FT) information from databases like SWISS-PROT for enhanced function prediction.
  • To compare the performance of this new approach against methods using only keyword (KW) information.

Main Methods:

  • The method correlates short sequence signals with functional annotations from the SWISS-PROT database.
  • It utilizes both keyword (KW) and feature (FT) information, where FT specifies the location of protein characteristics.
  • Function assignment requires sequence similarity within the position specified by the FT field.

Main Results:

  • Exhaustive tests were conducted on sequences with and without known homologs (cluster and singleton sets).
  • Using feature (FT) information in addition to keywords resulted in significantly 'cleaner' function assignments compared to using keywords alone.
  • The positional information provided by FT fields proved critical for accurate annotation.

Conclusions:

  • Incorporating domain (FT) information significantly refines protein function prediction accuracy.
  • This approach offers a more precise method for annotating protein functions, particularly for novel or poorly characterized sequences.
  • The developed method enhances the reliability of functional assignments in bioinformatics.