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Related Concept Videos

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 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...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Protein Folding01:22

Protein Folding

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Related Experiment Video

Updated: May 20, 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

Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and

Mark A Hallen1, Daniel A Keedy, Bruce R Donald

  • 1Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA.

Proteins
|July 24, 2012
PubMed
Summary

A new computational method, DEEPer, accurately models protein conformations by incorporating extensive backbone flexibility and ensembles. This advances protein design and drug discovery by enabling more precise predictions of mutations and ligand interactions.

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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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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein design

Background:

  • Accurate protein conformation modeling is crucial for computational protein and drug design.
  • Existing algorithms like DEE/A* find global minimum-energy conformations (GMEC) with limitations in backbone flexibility and ensemble modeling.

Purpose of the Study:

  • Introduce DEEPer (Dead-End Elimination with Perturbations), a novel algorithm for enhanced protein conformation modeling.
  • Improve the accuracy and scope of computational protein design by addressing limitations in previous methods.

Main Methods:

  • DEEPer combines Dead-End Elimination with Perturbations to handle extensive backbone flexibility and ensembles.
  • Incorporates local backbone motions (shear) and an acceleration technique (indirect pruning).
  • Provably finds GMEC or conformations within a specified energy window.

Main Results:

  • DEEPer consistently identified lower-energy conformations than previous methods across 67 benchmark tests on 64 proteins.
  • Demonstrated ability to model larger backbone conformational changes and realistic ensembles.
  • Significantly improved accuracy in modeling protein mutations and protein-ligand interactions.

Conclusions:

  • DEEPer offers significant advantages for accurate protein modeling, surpassing previous methods.
  • Enables more sophisticated computational protein design by handling complex backbone dynamics.
  • Facilitates enhanced prediction of mutation effects and ligand binding in drug discovery.