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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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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ProtorP: a protein-protein interaction analysis server.

Christopher Reynolds1, David Damerell, Susan Jones

  • 1Department of Biochemistry, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, Brighton BN1 9QG, UK.

Bioinformatics (Oxford, England)
|November 13, 2008
PubMed
Summary
This summary is machine-generated.

The PROTORP server analyzes protein-protein interactions using 3D structures, calculating key physical and chemical properties that influence binding energy. This tool aids in characterizing protein associations and comparing them to existing datasets.

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08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biochemistry

Background:

  • Protein-protein interactions are fundamental to cellular processes.
  • Understanding these associations is crucial for drug discovery and systems biology.
  • The Protein Data Bank (PDB) contains numerous protein association structures.

Purpose of the Study:

  • To introduce the PROTORP server for analyzing protein-protein associations.
  • To provide a tool for calculating biophysical parameters of protein interaction sites.
  • To enable comparison of analyzed interactions with existing datasets.

Main Methods:

  • Analysis of protein-protein associations in 3D structures.
  • Calculation of physical and chemical parameters at protein interaction sites.
  • Utilizing datasets from the Protein Data Bank (PDB) and user-uploaded files.

Main Results:

  • PROTORP calculates parameters like size, shape, intermolecular bonding, residue/atom composition, and secondary structure contributions.
  • The server facilitates analysis of individual or large datasets of protein associations.
  • Calculated properties can be compared against provided distributions of different protein association classes.

Conclusions:

  • PROTORP offers an efficient method for characterizing protein-protein associations.
  • The server allows contextualization of new or existing protein interaction data.
  • It aids in understanding the binding energy contributions of various interaction site properties.