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Related Concept Videos

Protein Networks02:26

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
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...

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

Published on: July 14, 2015

Optimizing a global alignment of protein interaction networks.

Leonid Chindelevitch1, Cheng-Yu Ma, Chung-Shou Liao

  • 1Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Computer Science and Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu 30013, Taiwan.

Bioinformatics (Oxford, England)
|September 20, 2013
PubMed
Summary
This summary is machine-generated.

We introduce PISwap, a novel algorithm for optimizing protein interaction network alignments. This method refines existing techniques, offering robust and flexible insights into species evolution and functional orthologs.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Global alignment of protein interaction networks is crucial for understanding inter-species protein relationships and identifying functional orthologs.
  • This alignment also provides valuable insights into evolutionary dynamics.

Purpose of the Study:

  • To propose and evaluate PISwap, a novel algorithm for optimizing global pairwise alignments of protein interaction networks.
  • To demonstrate the algorithm's efficiency, robustness to data noise, and flexibility for various network alignment applications.

Main Methods:

  • PISwap utilizes a local optimization heuristic to refine initial network alignments.
  • The algorithm iteratively adjusts alignments by integrating network topology and sequence information.
  • It can build upon various existing network alignment approaches.

Main Results:

  • PISwap efficiently refines established alignment techniques with minimal computational overhead.
  • The algorithm demonstrates robustness when applied to noisy protein interaction data.
  • PISwap yields significant insights into the evolutionary dynamics of related species.

Conclusions:

  • PISwap offers an effective and flexible approach for global protein interaction network alignment.
  • The algorithm enhances our understanding of protein function, orthology, and evolutionary relationships.
  • PISwap is freely available for non-commercial use, facilitating broader research applications.