Related Experiment Video
Updated: Jun 14, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
1National Institute of Chemistry, Ljubljana, Slovenia.
Bioinformatics (Oxford, England)
|March 23, 2010
Summary
This study introduces ProBiS, a novel algorithm for detecting protein binding sites using local 3D surface patterns. ProBiS identifies structurally similar sites, aiding in the discovery of functionally important regions on proteins.
Area of Science:
- Structural bioinformatics
- Computational biology
- Biochemistry
Background:
- Detecting protein binding sites is crucial for understanding protein function and drug discovery.
- Traditional methods often rely on sequence or global structural similarity, which can miss conserved functional sites.
- Exploiting local 3D patterns of physicochemical properties offers a complementary approach.
Purpose of the Study:
- To develop and present an algorithm, ProBiS, for identifying structurally similar sites on protein surfaces.
- To enable the detection of protein binding sites that may not be conserved in sequence or global structure.
Main Methods:
- ProBiS employs local surface structure alignment to compare query proteins against a database of 3D structures.
- An efficient maximum clique algorithm is used to identify proteins with local structural similarities.
- The method detects patterns of physicochemical properties on protein surfaces with sub-residue precision.
Main Results:
- ProBiS successfully identifies structurally similar sites, revealing local patterns of physicochemical properties.
- The algorithm generates structure-based alignments and calculates similarity scores, visualized on the protein surface.
- Successful application in detecting protein-protein, protein-small ligand, and protein-DNA binding sites.
Conclusions:
- ProBiS is an effective tool for detecting protein binding sites based on local surface structural and physicochemical similarities.
- The algorithm enhances the ability to find functional sites, particularly those lacking sequence conservation.
- The ProBiS software is publicly available as a free web tool for academic users.
More Related Videos
06:50Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Related Concept Videos
01:49Conserved 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...
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...
01:49Conserved 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...
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...
02:04Protein-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...
02:04Protein-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...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
02:26Protein 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,...
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,...