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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...
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...

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Ligand binding site detection by local structure alignment and its performance complementarity.

Hui Sun Lee1, Wonpil Im

  • 1Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States.

Journal of Chemical Information and Modeling
|August 21, 2013
PubMed
Summary
This summary is machine-generated.

Predicting ligand binding sites (BS) is crucial for drug design. A new local structure alignment (LSA) tool, G-LoSA, improves precision by focusing on local protein structures, complementing existing methods for better accuracy.

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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

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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

Area of Science:

  • Computational Biology
  • Structural Biology
  • Drug Discovery

Background:

  • Accurate identification of ligand binding sites (BS) is essential for protein function studies and structure-based drug design.
  • Existing template-based methods using global structure alignment (GSA) show promise but can be improved by incorporating local structure alignment (LSA), as binding sites are local features.

Purpose of the Study:

  • To develop and validate a novel template-based ligand BS prediction method incorporating LSA.
  • To assess the performance of the new method, G-LoSA, against existing GSA-based and geometry-based methods.
  • To develop a consensus scoring method combining complementary approaches for enhanced prediction accuracy.

Main Methods:

  • Development of G-LoSA, a local structure alignment (LSA) tool for template-based ligand BS prediction.
  • Validation using a large benchmark dataset comparing G-LoSA against TM-align (GSA-based) and fpocket (geometry-based).
  • Creation of a consensus scoring method, CMCS-BSP, integrating predictions from complementary methods.

Main Results:

  • G-LoSA demonstrates higher precision in predicting drug-like ligand positions in single-chain protein targets compared to TM-align.
  • G-LoSA excels at detecting conserved local structures across proteins with varying global folds.
  • The consensus scoring method, CMCS-BSP, shows improved overall prediction accuracy by combining complementary prediction strategies.

Conclusions:

  • Local structure alignment (LSA) offers a valuable complementary approach to GSA for ligand binding site prediction.
  • G-LoSA provides precise predictions, particularly for conserved local structural motifs.
  • The developed consensus scoring method (CMCS-BSP) enhances the robustness and accuracy of ligand binding site prediction.