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Related Concept Videos

Additional Subnuclear Structures02:10

Additional Subnuclear Structures

The eukaryotic nucleus is a double membrane-bound organelle that contains nearly all of the cell’s genetic material in the form of chromosomes. It is rightly called the “brain” of the cell as it shoulders the responsibility of responding to various physiological processes, stress, altered metabolic conditions, and other cellular signals. 
The nucleus contains many membrane-less subnuclear organelles or nuclear bodies, such as nucleoli, Cajal bodies, speckles, paraspeckles, etc. These nuclear...
Additional Subnuclear Structures02:10

Additional Subnuclear Structures

The eukaryotic nucleus is a double membrane-bound organelle that contains nearly all of the cell’s genetic material in the form of chromosomes. It is rightly called the “brain” of the cell as it shoulders the responsibility of responding to various physiological processes, stress, altered metabolic conditions, and other cellular signals. 
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Cleavage and Blastulation

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Protein Organization01:13

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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.
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3D Printing of Biomolecular Models for Research and Pedagogy
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Creating supersecondary structures with BuildBeta.

Silvia Crivelli1, Nelson Max

  • 1Department of Computer Science, University of California, Davis, CA, USA. SNCrivelli@lbl.gov

Methods in Molecular Biology (Clifton, N.J.)
|September 19, 2012
PubMed
Summary
This summary is machine-generated.

BuildBeta enhances protein structure prediction for beta sheets by improving sampling methods. This software tackles challenging protein targets, advancing template-free modeling techniques.

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Area of Science:

  • Computational biology
  • Structural bioinformatics

Background:

  • Protein structure prediction is crucial for understanding biological function.
  • Proteins containing beta sheets present significant prediction challenges due to complex long-range interactions.
  • Accurate modeling of protein conformations is essential for drug discovery and disease research.

Purpose of the Study:

  • To introduce BuildBeta, a novel feature in ProteinShop software.
  • To enhance the sampling capabilities of template-free modeling for beta-sheet-rich proteins.
  • To address challenging protein targets from the Critical Assessment of Techniques for Protein Structure Prediction (CASP9).

Main Methods:

  • BuildBeta utilizes amino acid sequences and secondary structure predictions for conformational sampling.
  • It integrates with and augments existing template-free modeling approaches.
  • The method focuses on improving the sampling of long-range strand pairings in beta sheets.

Main Results:

  • BuildBeta demonstrates improved sampling for difficult protein targets, including those from CASP9.
  • The software effectively leverages successful template-free modeling strategies.
  • Enhanced sampling leads to more accurate predictions for beta-sheet-rich protein structures.

Conclusions:

  • BuildBeta offers a significant advancement in predicting complex protein structures, particularly those with beta sheets.
  • The software has the potential to improve the accuracy and efficiency of protein structure prediction.
  • Ongoing development aims to further refine supersecondary structure generation quality.