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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...
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,...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Constructing patch-based ligand-binding pocket database for predicting function of proteins.

Lee Sael1, Daisuke Kihara

  • 1Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

BMC Bioinformatics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

Patch-Surfer, a protein pocket comparison method, accurately predicts binding ligands for proteins with unknown functions. This tool effectively identifies potential ligand interactions even without sequence similarity to known proteins.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Many solved protein structures lack known functions due to absent sequence/structural similarity to known proteins.
  • Predicting small ligand molecules that bind to proteins can provide functional clues for these unknown proteins.

Purpose of the Study:

  • To extend the Patch-Surfer method's capability in predicting binding ligands for proteins of unknown function.
  • To enhance the ligand binding pocket database for more diverse ligand predictions.

Main Methods:

  • Developed an alignment-free, local surface-based pocket comparison method (Patch-Surfer).
  • Extended the Patch-Surfer database to include diverse ligand binding pockets from the Protein Data Bank.
  • Tested Patch-Surfer on 75 non-homologous proteins against a database of 9393 pockets representing 2707 ligand types.

Main Results:

  • Patch-Surfer achieved an average enrichment factor exceeding 20.0 at 0.1%.
  • The prediction accuracy was independent of the query protein's sequence similarity to database entries.
  • Demonstrated successful ligand prediction even for proteins lacking homologous structures in the database.

Conclusions:

  • Patch-Surfer is effective in predicting binding ligands for proteins with unknown functions.
  • The method's performance is robust, not relying on sequence homology.
  • This approach aids in elucidating protein functions and facilitates drug discovery efforts.