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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 and Protein Structures02:15

Protein and Protein Structures

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.
A protein's shape is critical to its function. For example, an enzyme can...
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.
A protein's shape is critical to its function. For example, an enzyme can...
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...

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Related Experiment Video

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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

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

Pablo Gainza1, Kyle E Roberts, Ivelin Georgiev

  • 1Department of Computer Science, Duke University, Durham, North Carolina, USA.

Methods in Enzymology
|February 21, 2013
PubMed
Summary

We developed OSPREY, a protein redesign software. It enhances in silico protein modeling using flexibility, ensembles, and optimal search for predicting mutations and binding affinity.

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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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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Computational biology
  • Protein engineering
  • Biophysics

Background:

  • Protein redesign algorithms are crucial for understanding protein function and developing new therapeutics.
  • Accurate in silico modeling requires capturing conformational changes and binding dynamics.
  • Existing methods often lack the flexibility and global optimization needed for realistic predictions.

Purpose of the Study:

  • To introduce a novel suite of protein redesign algorithms and the OSPREY software.
  • To demonstrate the importance of enhanced flexibility, ensemble modeling, and globally optimal search in protein design.
  • To showcase OSPREY's application in predicting resistance mutations and understanding protein-ligand interactions.

Main Methods:

  • Development of protein redesign algorithms incorporating backbone and side-chain flexibility.
  • Modeling proteins and ligands as ensembles of low-energy structures to approximate binding affinity.
  • Implementation of a globally optimal search strategy for protein design predictions.

Main Results:

  • OSPREY successfully models conformational changes induced by mutations.
  • Ensemble modeling improves the approximation of binding affinity.
  • Globally optimal search guarantees optimal predictions based on the input model.
  • Prospective experimental validation confirms OSPREY's accuracy in predicting resistance mutations.

Conclusions:

  • The OSPREY suite provides a powerful tool for realistic in silico protein modeling and redesign.
  • Improved flexibility, ensemble modeling, and provable optimality are essential for accurate prediction of protein behavior.
  • OSPREY has demonstrated utility in biomedically relevant applications, including mutation prediction.