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Related Concept Videos

Protein Organization01:24

Protein Organization

6.0K
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.
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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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Protein-protein Interfaces

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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...
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Protein Families02:47

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein Networks02:26

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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.
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Updated: May 9, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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ProteinsPlus: a publicly available resource for protein structure mining.

Christiane Ehrt1, Thorben Schulze1, Joel Graef1

  • 1University of Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761 Hamburg, Germany.

Nucleic Acids Research
|May 6, 2025
PubMed
Summary
This summary is machine-generated.

ProteinsPlus is a web server for protein structure analysis and modeling, focusing on protein-ligand interactions. Recent updates enhance its utility for structure-based drug design and future development.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Bioinformatics

Background:

  • ProteinsPlus is an evolving web server providing tools for protein structure analysis and modeling.
  • It focuses on protein-ligand interactions, utilizing data from the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.
  • The server has expanded its capabilities since its 2017 launch.

Purpose of the Study:

  • To present recent updates and novel methods integrated into the ProteinsPlus web server.
  • To demonstrate the applicability of these tools in real-life structure-based design projects.
  • To outline future development plans for enhanced usability and maintainability.

Main Methods:

  • Integration of new methods for binding site detection and solvent channel prediction in crystallographic structures.
  • Updates to existing tools for 2D protein-ligand interaction depiction and binding site mining.
  • Utilizing experimental PDB structures and predicted structures from AlphaFold as input.

Main Results:

  • The web server now offers six methods for protein structure analysis, four for PDB mining, and five for protein-ligand complex modeling.
  • Novel methods for detecting binding sites and predicting solvent channels have been implemented.
  • Updated tools facilitate enhanced visualization and analysis of protein-ligand interactions.

Conclusions:

  • The enhanced ProteinsPlus web server provides valuable tools for modern structure-based design.
  • Recent updates improve the detection and analysis of protein-ligand interactions.
  • Future redesign aims to increase inter-usability, maintainability, and future-proof the platform.