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Related Concept Videos

Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
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...
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 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...
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...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

Convergent algorithms for protein structural alignment.

Leandro Martínez1, Roberto Andreani, José Mario Martínez

  • 1Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil. leandromartinez98@gmail.com

BMC Bioinformatics
|August 24, 2007
PubMed
Summary
This summary is machine-generated.

This study introduces a novel Low Order Value Optimization (LOVO) approach for protein structural alignment, ensuring score maximization and convergence. This method refines protein folding maps and aids in developing function-correlated scores.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Algorithm Development

Background:

  • Existing protein structural alignment algorithms often lack theoretical convergence guarantees.
  • Maximizing scoring functions in protein alignment is a key challenge without guaranteed optimal solutions.
  • A need exists for convergent algorithms to refine protein folding maps and develop function-based scoring.

Purpose of the Study:

  • To interpret protein alignment as a Low Order Value Optimization (LOVO) problem.
  • To develop novel, convergent algorithms for protein structural alignment.
  • To enhance the reliability of scoring function maximization for improved biological insights.

Main Methods:

  • Interpreted protein alignment as a Low Order Value Optimization (LOVO) problem.
  • Developed two algorithms based on continuous optimization methods.
  • One algorithm combines Dynamic Programming with Newtonian methods; the second uses a fast C-alpha atom correspondence procedure.

Main Results:

  • The developed algorithms are convergent and guarantee score increase at each iteration.
  • Solutions obtained represent critical points of the scoring functions.
  • Algorithms demonstrated high effectiveness in maximizing the STRUCTAL score.

Conclusions:

  • The LOVO interpretation provides a robust theoretical framework for convergent protein alignment algorithms.
  • Algorithms reliably maximize the STRUCTAL score and can optimize other distance-dependent scores.
  • This approach aids in refining protein fold maps, developing function-correlated scores, and addressing general structural superposition problems.