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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...
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...
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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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence

Jianyi Yang1, Ambrish Roy, Yang Zhang

  • 1Department of Computational Medicine and Bioinformatics and Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA.

Bioinformatics (Oxford, England)
|August 27, 2013
PubMed
Summary
This summary is machine-generated.

We developed new computational methods to accurately predict protein-ligand binding sites, crucial for understanding protein function and accelerating drug discovery. Combining these methods, COACH, significantly improves prediction accuracy across diverse datasets.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Protein-ligand binding site identification is vital for protein function annotation and drug discovery.
  • Existing methods lack optimal prediction capabilities across diverse protein types.
  • Combining complementary prediction methods offers a reliable solution.

Purpose of the Study:

  • To develop novel computational methods for accurate protein-ligand binding site prediction.
  • To create a consensus approach by combining individual prediction methods.
  • To enhance genome-wide structure-based function annotations.

Main Methods:

  • Developed TM-SITE (binding-specific substructure comparison) and S-SITE (sequence profile alignment) methods.
  • Tested methods on 500 non-redundant proteins with 814 ligands.
  • Created a consensus approach (COACH) by integrating TM-SITE, S-SITE, and other structure-based programs.

Main Results:

  • TM-SITE and S-SITE recognized over 51% of binding residues with significantly higher MCC than state-of-the-art methods.
  • The COACH consensus approach increased MCC by 15% compared to individual predictions.
  • COACH consistently ranked first in 22 datasets in the COMEO experiment, outperforming the second-best method by 22.5% AUC.

Conclusions:

  • TM-SITE and S-SITE provide robust protein-ligand binding site recognition.
  • The COACH consensus approach represents a significant advancement in binding site prediction.
  • The developed methods are ready for large-scale, structure-based protein function annotation.