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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...
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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,...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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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.
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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

A collaborative environment for developing and validating predictive tools for protein biophysical characteristics.

Michael A Johnston1, Damien Farrell, Jens Erik Nielsen

  • 1School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland. michael.ap.johnston@gmail.com

Journal of Computer-Aided Molecular Design
|April 6, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a collaborative environment to bridge the gap between experimentalists and theoreticians in biology. It enhances the development and validation of protein biophysical characteristic prediction tools.

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09:51

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05:08

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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Area of Science:

  • Computational biology
  • Biophysics
  • Bioinformatics

Background:

  • Effective collaboration between experimentalists and theoreticians is vital for advancing biological understanding and predictive modeling.
  • Barriers to information exchange hinder the integration of computational tools and experimental data.
  • Accessible data sharing and computational results are essential for community-wide progress.

Purpose of the Study:

  • To present a prototype collaborative environment for developing and validating predictive tools for protein biophysical characteristics.
  • To facilitate the integration of theoretical methods with experimental data.
  • To improve the accessibility and usability of computational tools for experimentalists.

Main Methods:

  • Development of a Python-based integration module for remote program management by theoreticians.
  • Implementation of PEATDB for storing and sharing experimental data from protein biophysical characterization.
  • Integration of PEATSA, a web-based prediction service, into PEATDB.

Main Results:

  • A functional prototype collaborative environment integrating experimental data and predictive tools.
  • Demonstrated ease of use for experimentalists in applying computational tools.
  • Successful validation of the environment using the Potapov dataset for protein stability prediction.

Conclusions:

  • The developed environment effectively supports the creation and validation of predictive models for protein biophysical properties.
  • Enhanced collaboration between disciplines accelerates the development of theoretical methods.
  • The platform promotes data sharing and computational accessibility, benefiting the wider scientific community.