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Related Concept Videos

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,...
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,...
Protein Organization01:24

Protein 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.
Protein Organization01:24

Protein 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.

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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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PrePPI: a structure-informed database of protein-protein interactions.

Qiangfeng Cliff Zhang1, Donald Petrey, José Ignacio Garzón

  • 1Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia Initiative in Systems Biology, Columbia University, New York, NY 10032, USA.

Nucleic Acids Research
|November 30, 2012
PubMed
Summary

PrePPI integrates predicted and experimental protein-protein interactions (PPIs) using a Bayesian approach. This database provides probabilities for PPIs, aiding in the identification of novel interactions and structural insights.

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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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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Published on: March 3, 2015

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • Integrating diverse data sources for PPI prediction remains a challenge.
  • Existing databases often lack comprehensive probability assignments for interactions.

Purpose of the Study:

  • To develop a comprehensive database of protein-protein interactions (PPIs).
  • To assign confidence scores to both predicted and experimentally determined PPIs.
  • To provide structural models for identified PPIs.

Main Methods:

  • Utilized a Bayesian framework to combine predicted and experimentally determined PPIs.
  • Calculated likelihood ratios (LRs) from structural, functional, evolutionary, and expression data for predictions.
  • Compiled experimentally validated PPIs from public databases, assigning LRs.
  • Integrated LRs from both sources to generate a final probability for each PPI.

Main Results:

  • The PrePPI database contains approximately 2 million PPIs with a probability > 0.1.
  • Approximately 60,000 yeast PPIs and 370,000 human PPIs are considered high confidence (probability > 0.5).
  • Structural models are provided for a significant number of PPIs.

Conclusions:

  • PrePPI offers an integrated resource for examining known and potential novel PPIs.
  • The database provides valuable confidence scores for PPIs, enhancing reliability.
  • Structural insights into PPIs are made accessible through the PrePPI resource.