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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as 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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence 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...

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Predicting ligand binding residues and functional sites using multipositional correlations with graph theoretic

Alvaro J González1, Li Liao, Cathy H Wu

  • 1Computer and Information Sciences Department, University of Delaware, 101 Smith Hall, Newark, DE 19716, USA. alvaro@cis.udel.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 26, 2011
PubMed
Summary

This study introduces a novel computational method for identifying protein binding and functional sites by analyzing evolutionary correlations. Accounting for multipositional correlations significantly enhances prediction accuracy for these crucial protein regions.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Ligand binding residues and functional sites are critical for protein structure and function.
  • Evolutionary conservation and positional correlations are key indicators of these sites.
  • Existing methods may not fully capture the impact of multipositional correlations.

Purpose of the Study:

  • To develop a new computational method for predicting ligand binding residues and functional sites in protein sequences.
  • To investigate the role of correlations among multiple positions in sequence analysis.
  • To improve the accuracy of identifying functionally important residues.

Main Methods:

  • Utilized graph theoretic clustering to analyze sequence data.
  • Employed kernel-based canonical correlation analysis (kCCA) to identify correlations.
  • Integrated evolutionary characterization with structure-based functional classification within protein families.

Main Results:

  • The developed method successfully identifies residues with strong correlations.
  • Prediction accuracy, measured by Receiver Operating Characteristic (ROC) scores, showed significant improvement.
  • The enhancement in accuracy was attributed to the consideration of multipositional correlations.

Conclusions:

  • The new computational approach effectively predicts ligand binding and functional sites.
  • Incorporating multipositional correlations is crucial for accurate site prediction in proteins.
  • This method offers a significant advancement in bioinformatics tools for protein analysis.