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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,...
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...
pV-Diagrams01:18

pV-Diagrams

The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...

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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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VASCo: computation and visualization of annotated protein surface contacts.

Georg Steinkellner1, Robert Rader, Gerhard G Thallinger

  • 1Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, Graz, Austria. georg.steinkellner@uni-graz.at

BMC Bioinformatics
|January 27, 2009
PubMed
Summary

VASCo is a new software tool that visualizes protein-protein interactions and surface properties. It aids in analyzing biological and crystal contacts by comparing molecular surfaces.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Crystallographic data offer insights into protein-protein contacts, crucial for cellular processes.
  • Understanding protein interactions aids in studying biologically relevant protein oligomerization.
  • Visualizing crystal and biological contacts with surface properties enhances interaction analysis.

Purpose of the Study:

  • To introduce VASCo, a program package for calculating and visualizing protein surface properties.
  • To focus on protein-protein interactions using surface point distance calculations.
  • To enable comparison of surfaces between aligned molecules.

Main Methods:

  • VASCo calculates protein surface properties and visualizes annotated surfaces.
  • Protein-protein interactions are determined via surface point distance calculations.
  • Molecular properties like electrostatic potential and hydrophobicity are mapped onto surface points.

Main Results:

  • VASCo calculates molecular surfaces and properties using integrated and custom programs.
  • The package is modular and extensible for new property annotations.
  • Output is visualized in PyMOL via a custom plug-in.

Conclusions:

  • VASCo complements existing protein contact visualization tools.
  • It provides additional insights into biological and crystal contacts.
  • VASCo uniquely compares aligned molecular surfaces by point distances, aiding analysis of surface differences.