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Protein-protein Interfaces02:04

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 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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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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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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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: Mar 10, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Automated protein design: Landmarks and operational principles.

Anil Kumar1, Ranjit Ranbhor2, Kirti Patel3

  • 1Department of Chemistry, University of Toronto, ON, M5S3H6, Canada.

Progress in Biophysics and Molecular Biology
|December 17, 2016
PubMed
Summary

Automated protein design algorithms, leveraging computational advances, offer a tractable approach to creating novel protein sequences. This progress report details key milestones and operational principles in automated protein design.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Protein Engineering

Background:

  • Protein design has a 30-year history with many failures.
  • Advances in computing and algorithms have improved design practices.
  • The protein folding problem remains unsolved, but protein design is more tractable due to multiple sequence solutions for a single fold.

Purpose of the Study:

  • To present important landmarks in automated protein design attempts.
  • To provide an account of the operational principles in automated design methods.

Main Methods:

  • Implementation of automated design algorithms on pre-defined templates or novel folds.
  • Optimization through deterministic and heuristic search algorithms.

Main Results:

  • Significant advancements in automated design algorithms.
  • Progress in optimizing protein sequences for specific folds.

Conclusions:

  • Automated design methods represent a significant advancement in protein engineering.
  • Further development in algorithms and computational power will continue to drive progress in protein design.