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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...
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...
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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Published on: July 25, 2013

Identification of binding pockets in protein structures using a knowledge-based potential derived from local

Valerio Bianchi1, Pier Federico Gherardini, Manuela Helmer-Citterich

  • 1Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, Rome 00133, Italy.

BMC Bioinformatics
|April 28, 2012
PubMed
Summary

PDBinder identifies ligand binding sites by recognizing shared structural motifs in proteins. This knowledge-based method accurately predicts binding residues and clefts, outperforming existing computational approaches for protein annotation.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Identifying ligand binding sites is crucial for annotating proteins with unknown functions.
  • Unrelated binding sites can share small structural motifs that bind common chemical fragments.

Purpose of the Study:

  • To develop and evaluate a knowledge-based method for predicting ligand binding sites in proteins.
  • To assess the method's performance in identifying binding residues and locating binding clefts.

Main Methods:

  • PDBinder compares query proteins against a library of protein surface regions from the Protein Data Bank (PDB).
  • It calculates a propensity value for each residue, indicating its likelihood of being part of a ligand binding site.
  • The method was trained on 1356 protein-ligand complexes and tested on 239 holo and apo complex pairs.

Main Results:

  • PDBinder demonstrated superior performance compared to existing methods for both ligand binding residue prediction and binding site identification.
  • Achieved a Matthews Correlation Coefficient (MCC) of 0.313 and a Positive Predictive Value (PPV) of 0.413 on holo complexes.
  • On apo complexes, PDBinder yielded an MCC of 0.271 and a PPV of 0.372, showing effectiveness on unbound proteins.

Conclusions:

  • PDBinder significantly outperforms current methods for ligand binding site identification.
  • Its strong performance on unbound proteins is vital for practical applications where binding site location is unknown.
  • The PDBinder propensity score can be integrated with other algorithms to enhance overall predictive accuracy.