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Related Concept Videos

Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Fibrous Proteins00:55

Fibrous Proteins

Fibrous proteins are either long and narrow proteins or assemble to form long and thin structures. They contain repetitive units and usually consist of either alpha helices or beta sheets and, in rare cases, a mix of both. The amino acids in the primary structure often consist of repeating amino acid sequences. The role of fibrous proteins is primarily structural. Many are located in the extracellular matrix and are present in connective tissues to impart strength and joint mobility. They are...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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Protein Families

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 locations, protein...

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Low-homology protein threading.

Jian Peng1, Jinbo Xu

  • 1Toyota Technological Institute at Chicago, IL 60637, USA.

Bioinformatics (Oxford, England)
|June 10, 2010
PubMed
Summary
This summary is machine-generated.

A new profile-entropy scoring function improves low-homology protein threading by prioritizing structural data for proteins with limited homologous information. This method outperforms existing tools like HHpred on challenging targets.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Template-based protein modeling faces challenges in identifying correct templates and generating accurate sequence-template alignments.
  • Profile-based methods like HHpred excel at detecting remote homologs but struggle with low-homology proteins lacking sufficient database information.

Purpose of the Study:

  • To develop an improved protein threading method for low-homology proteins.
  • To address the limitations of existing methods when homologous information is scarce.

Main Methods:

  • Introduced a profile-entropy dependent scoring function for protein threading.
  • The scoring function dynamically adjusts feature importance based on available homologous information, prioritizing structure for low-homology cases.

Main Results:

  • The proposed threading method significantly outperforms HHpred and top CASP8 servers on low-homology proteins.
  • On CASP8 hard targets, the method shows competitive performance against leading servers, even without post-threading refinement.

Conclusions:

  • The profile-entropy dependent scoring function offers a robust solution for low-homology protein threading.
  • This approach enhances accuracy by leveraging structural information when homologous data is limited.