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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...
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 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...
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...
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...

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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

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.

Sriram Sankararaman1, Bryan Kolaczkowski, Kimmen Sjölander

  • 1Department of Computer Science, University of California, Berkeley, USA.

Nucleic Acids Research
|May 16, 2009
PubMed
Summary

The INTREPID web server accurately predicts functionally important protein residues, improving upon existing sequence-based methods for identifying catalytic sites and other functional residues.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Identifying functionally important residues in proteins is crucial for understanding biological mechanisms.
  • Existing sequence-based methods have limitations in predicting residue function, particularly for catalytic sites.

Purpose of the Study:

  • To introduce the INTREPID web server, a novel tool for predicting functionally important residues in proteins.
  • To evaluate INTREPID's performance in predicting catalytic residues compared to other methods.

Main Methods:

  • The INTREPID web server utilizes protein sequence input to gather homologs, construct multiple sequence alignments, and build phylogenetic trees.
  • The INTREPID method is applied to assign functional importance scores to each residue position.
  • Predicted residues are visualized on homologous 3D structures, highlighting spatial conservation patterns.

Main Results:

  • INTREPID demonstrates enhanced recall and precision in predicting catalytic residues compared to existing sequence-based approaches.
  • The server effectively identifies various types of functional residues beyond catalytic sites.
  • Visualization of predicted residues on 3D structures reveals spatial conservation patterns.

Conclusions:

  • The INTREPID web server provides a powerful and accurate method for predicting functionally important protein residues.
  • INTREPID offers significant improvements over traditional sequence-based prediction methods.
  • The tool aids in understanding protein function through the identification and spatial mapping of critical residues.