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Related Concept Videos

Protein Families02:47

Protein Families

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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-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-Protein Interfaces02:04

Protein-Protein Interfaces

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Protein Organization01:24

Protein Organization

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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.
The primary structure of a protein is its amino acid sequence....
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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Fast search algorithms for computational protein design.

Seydou Traoré1,2,3, Kyle E Roberts4, David Allouche5

  • 1Université De Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, Toulouse, F-31077, France.

Journal of Computational Chemistry
|February 3, 2016
PubMed
Summary
This summary is machine-generated.

Computational protein design (CPD) is accelerated using Cost Function Networks (CFN) integrated into the Osprey software. This enhances algorithms for faster exploration of protein sequence and conformational space.

Keywords:
computational protein designcomputer-aided protein designcost function networksdeterministic search methodsexact combinatorial optimizationglobal minimum energy conformationnear-optimal solutionssearch heuristics

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Area of Science:

  • Computational biology
  • Protein engineering
  • Bioinformatics

Background:

  • Computational protein design (CPD) faces challenges due to the vast search space of protein sequences and conformations.
  • Existing methods require significant computational resources for exploration.

Purpose of the Study:

  • To accelerate provable rigid backbone protein design methods.
  • To enhance the Osprey CPD package with advanced optimization technologies.

Main Methods:

  • Integration of Cost Function Network (CFN) processing into the Osprey software.
  • Development of new A* search strategies combining CFN lower bounds with side-chain positioning.
  • Application of these methods to accelerate existing DEE/A* algorithms within Osprey.

Main Results:

  • Achieved significant speedups in CPD algorithms by several orders of magnitude.
  • Enabled much faster enumeration of suboptimal protein sequences.
  • Demonstrated the ability to solve larger CPD problems with provable algorithms.

Conclusions:

  • CFN technology injection dramatically improves Osprey's performance for CPD.
  • The novel A* strategies enhance the efficiency of exploring protein design space.
  • These advancements make complex protein design problems more computationally tractable.