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Related Concept Videos

Protein Organization01:24

Protein Organization

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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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Accuracy and Precision01:52

Accuracy and Precision

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Scientists typically make repeated measurements of a quantity to ensure the quality of their findings and to evaluate both the precision and the accuracy of their results. Measurements are said to be precise if they yield very similar results when repeated in the same manner. A measurement is considered accurate if it yields a result that is very close to the true or the accepted value. Precise values agree with each other; accurate values agree with a true value.  Highly accurate...
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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.
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Conserved Binding Sites01:49

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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.
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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Uncertainty in Measurement: Accuracy and Precision03:37

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Scientists typically make repeated measurements of a quantity to ensure the quality of their findings and to evaluate both the precision and the accuracy of their results. Measurements are said to be precise if they yield very similar results when repeated in the same manner. A measurement is considered accurate if it yields a result that is very close to the true or the accepted value. Precise values agree with each other; accurate values agree with a true value. 
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Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules
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How precise are reported protein coordinate data?

Arun S Konagurthu1, Lloyd Allison1, David Abramson1

  • 1Clayton School of Computer Science and Information Technology, Monash University, Clayton, VIC 3800, Australia.

Acta Crystallographica. Section D, Biological Crystallography
|March 7, 2014
PubMed
Summary
This summary is machine-generated.

Protein atomic coordinates in the Worldwide Protein Data Bank (wwPDB) are often reported with higher precision than experimentally justified. Information theory reveals realistic coordinate precision is typically around 0.1 Å for C(α) atoms.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Atomic coordinates in the Worldwide Protein Data Bank (wwPDB) are crucial for understanding protein structure and function.
  • Current reporting practices may overstate the precision of experimentally determined protein structures.

Purpose of the Study:

  • To quantify the realistic precision of atomic coordinates deposited in the wwPDB.
  • To assess the information content and compressibility of protein coordinate data.

Main Methods:

  • Applied information theory and data compression techniques to analyze protein atomic coordinate data.
  • Studied a diverse set of protein structures determined at various resolutions.
  • Quantified randomness within coordinate data to estimate precision.

Main Results:

  • Determined that reported atomic coordinate precision often exceeds experimental reality.
  • On average, C(α) coordinates in selected protein structures are reliably determined to approximately 0.1 Å.
  • Information theory provides a robust method for assessing coordinate data quality.

Conclusions:

  • The realistic precision of protein atomic coordinates in the wwPDB is generally lower than reported.
  • Information-theoretic analysis offers a valuable tool for evaluating structural data quality.
  • Accurate precision estimates are vital for reliable structural biology research and drug design.