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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
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...
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...
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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RaptorX: exploiting structure information for protein alignment by statistical inference.

Jian Peng1, Jinbo Xu

  • 1Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL 60637, USA.

Proteins
|October 12, 2011
PubMed
Summary
This summary is machine-generated.

RaptorX improves protein modeling by using structural information from templates. This statistical method enhances alignment accuracy, especially when similar templates are scarce, though improvements in alignment and template selection are still needed.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Template-based protein modeling is crucial for predicting protein structures.
  • Accurate sequence-to-structure alignments are essential for reliable modeling.
  • Existing methods may struggle with limited or distant templates.

Purpose of the Study:

  • To present RaptorX, a novel statistical method for template-based protein modeling.
  • To analyze RaptorX's performance in the CASP9 competition.
  • To identify limitations and future research directions in template-based modeling.

Main Methods:

  • RaptorX employs single-template threading, alignment quality prediction, and multiple-template threading.
  • The method leverages structural information from one or more templates.
  • Performance was evaluated using data from the Critical Assessment of protein Structure Prediction (CASP) 9.

Main Results:

  • Exploiting template structural information significantly improves protein threading accuracy.
  • RaptorX demonstrated effectiveness, particularly when closely related templates were unavailable.
  • Analysis revealed substantial room for improvement in sequence-template alignment and template selection strategies.

Conclusions:

  • Template structural information is a valuable asset in protein modeling, even with distant templates.
  • Further advancements are needed in alignment algorithms and template selection heuristics.
  • RaptorX provides a robust framework, with ongoing research focused on addressing identified bottlenecks.