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Related Concept Videos

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...
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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Updated: May 14, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Multistate protein design using CLEVER and CLASSY.

Christopher Negron1, Amy E Keating

  • 1Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

Methods in Enzymology
|February 21, 2013
PubMed
Summary
This summary is machine-generated.

Computational tools like cluster expansion accelerate protein design by simplifying complex energy calculations. This technique maps atomic coordinates to sequence-based functions, enabling faster scoring and novel search strategies for multistate protein design.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational biology
  • Protein engineering
  • Biophysics

Background:

  • Structure-based protein design holds significant promise but faces challenges in accurate structure scoring and efficient sequence-structure searching.
  • Current methods for evaluating protein sequence-energy relationships are often computationally intensive, limiting the scope of design explorations.
  • The vast search spaces in protein design necessitate faster computational approaches.

Purpose of the Study:

  • To introduce computational tools that significantly accelerate protein design processes.
  • To present cluster expansion as a method for simplifying complex protein energy functions.
  • To demonstrate the application of these tools in multistate protein design.

Main Methods:

  • Cluster expansion is employed to transform complex, three-dimensional atomic coordinate-dependent functions into simplified sequence-dependent functions.
  • The sequence-energy relationship is approximated as a linear function of sequence variables, trained on example data.
  • The CLEVER software is utilized to generate cluster-expanded scoring functions from existing procedures.
  • The CLASSY method is applied to implement cluster-expanded potentials for multistate protein design.

Main Results:

  • Cluster expansion dramatically speeds up scoring computations compared to traditional all-atom methods.
  • The simplified scoring functions facilitate the implementation of advanced search strategies.
  • Cluster expansion has demonstrated utility in protein design problems involving multiple conformational states.

Conclusions:

  • Cluster expansion offers a powerful approach to overcome computational bottlenecks in structure-based protein design.
  • The developed computational tools (CLEVER and CLASSY) enable efficient multistate protein design.
  • This methodology significantly enhances the feasibility and scope of protein engineering applications.