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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.
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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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

Accuracy analysis of multiple structure alignments.

Christoph Berbalk1, Christine S Schwaiger, Peter Lackner

  • 1Department of Molecular Biology, University of Salzburg, Austria.

Protein Science : a Publication of the Protein Society
|July 22, 2009
PubMed
Summary
This summary is machine-generated.

Evaluating multiple structure alignment (MStA) programs on difficult protein cases revealed significant performance variations. While the best methods achieve 84% accuracy, users should combine tools for optimal results in protein science.

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The ITS2 Database
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Published on: March 12, 2012

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Area of Science:

  • Protein science
  • Structural bioinformatics
  • Computational biology

Background:

  • Protein structure alignment is crucial for understanding protein relationships, function, and evolution.
  • Numerous pairwise and multiple structure alignment (MStA) programs exist, but their performance on challenging datasets is not well-defined.
  • Users need reliable estimates of alignment accuracy for effective application of these tools.

Purpose of the Study:

  • To evaluate the performance and limitations of current multiple structure alignment (MStA) programs.
  • To assess the correctness and applicability of different MStA methods on difficult protein structures.
  • To provide insights into the reliability of existing protein structure alignment tools.

Main Methods:

  • Compilation of a test suite comprising difficult-to-align proteins from literature and the SISYPHUS database.
  • Evaluation of various MStA programs using this test suite, focusing on alignment correctness and general limitations.
  • Quantitative analysis of the percentage of correctly aligned core positions for each method.

Main Results:

  • Significant variability in performance was observed among different MStA programs, with correctness ranging from 44% to 75% for core positions.
  • When considering the best result from any single method per test case, the accuracy increased to 84%.
  • Current MStA methods demonstrate applicability to challenging alignment scenarios, but substantial room for improvement exists.

Conclusions:

  • Existing MStA methods can handle difficult protein structure alignment tasks, but their accuracy and practicality vary considerably.
  • Relying on a single MStA program is not recommended; combining multiple methods may yield better results.
  • Future developments should focus on improving both the correctness and usability of MStA tools, potentially through integrated approaches.