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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Ligand Binding Sites02:40

Ligand Binding Sites

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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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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein Networks02:26

Protein Networks

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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,...
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Exploring Binding Sites on Proteins for Function Prediction Using the PoSSuM Databases.

Kentaro Tomii1, Kazuyoshi Ikeda2,3

  • 1Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan. k-tomii@aist.go.jp.

Methods in Molecular Biology (Clifton, N.J.)
|July 29, 2025
PubMed
Summary
This summary is machine-generated.

The PoSSuM database and its extensions (PoSSuMds, PoSSuMAg, PoSSuMAF) offer valuable tools for predicting protein functions and aiding drug discovery by analyzing protein-ligand binding site similarities using 3D structures.

Keywords:
AlphaFoldAntibody–antigen interactionBinding sitesDatabaseDrug discoveryLigandsPoSSuMProtein–ligand interactionSimilarity search

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Drug discovery

Background:

  • Protein function is intrinsically linked to its interactions with other molecules.
  • Analyzing protein-ligand complex structures aids in predicting biological functions and advancing drug discovery.
  • Existing databases provide valuable data on protein-ligand interactions.

Purpose of the Study:

  • To introduce and demonstrate the utility of the PoSSuM database and its related resources.
  • To facilitate the prediction of biological functions and support drug discovery and development efforts.
  • To showcase the application of these databases for analyzing protein binding sites.

Main Methods:

  • Construction and release of the PoSSuM database, compiling similarity search results for protein binding sites based on 3D structures.
  • Development of PoSSuMds for drug binding site similarity searches.
  • Expansion to PoSSuMAg for antibody-antigen binding site similarity and PoSSuMAF for binding sites in AlphaFold-predicted human protein structures.

Main Results:

  • The PoSSuM database provides compiled similarity search results for known and putative protein binding sites.
  • PoSSuMds, PoSSuMAg, and PoSSuMAF extend these capabilities to drug binding sites, antibody-antigen interactions, and predicted protein structures.
  • These databases enable efficient searching for similar binding sites across various protein types and contexts.

Conclusions:

  • The PoSSuM suite of databases offers powerful resources for structural bioinformatics and drug discovery.
  • Utilizing these databases can significantly enhance the prediction of protein functions and the identification of drug candidates.
  • The presented examples illustrate practical applications for leveraging these computational tools.