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When an object's velocity changes over time, the total distance traveled can be determined by summing small displacement intervals over short increments. This approach approximates the true distance through numerical summation and the use of integral calculus. An estimate of the total displacement can be obtained by measuring velocity at regular intervals and multiplying each value by the corresponding time step.If a runner accelerates over the first three seconds of a race, speed measurements...
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In geometry, measuring the direct distance between two points on a plane is essential in various practical and theoretical applications. Whether in navigation, engineering, or computer graphics, determining the shortest path between two locations involves using the distance formula. This formula is derived from the Pythagorean Theorem, which relates the lengths of the sides of a right triangle. On a coordinate plane, the horizontal and vertical distances between two points serve as the legs of...
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To achieve precise distance measurements, especially in surveying and construction, certain corrections must be applied to account for potential sources of error like the standardization errors, temperature variations, and slope adjustments.Standardization error emerges when measurement equipment undergoes changes, such as wear, repairs, or weather impacts. To address this, surveyors compare the equipment’s readings to a standard. This process identifies any deviation that might lead to...
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Quantifying Intermembrane Distances with Serial Image Dilations
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D2N: Distance to the native.

Avinash Mishra1, Prashant Singh Rana2, Aditya Mittal1

  • 1Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India.

Biochimica Et Biophysica Acta
|July 27, 2014
PubMed
Summary
This summary is machine-generated.

A new metric, D2N (distance to the native), predicts protein structure accuracy without needing the native structure. This tool helps assess computational biology predictions, crucial for understanding protein structures.

Keywords:
DecoyNativeProtein foldingQuality assessment

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • Root-mean-square-deviation (RMSD) is vital for evaluating protein structure prediction algorithms (PSPAs).
  • Accurately measuring the deviation of predicted protein structures from native structures is challenging without experimental data.
  • Developing accurate PSPAs is a central goal in computational biology.

Purpose of the Study:

  • To develop a novel metric, D2N (distance to the native), for predicting the RMSD of a protein structure.
  • To enable the assessment of protein structure quality without knowledge of the native structure.
  • To provide a tool for evaluating predicted protein structures in the absence of experimental data.

Main Methods:

  • Combined physico-chemical properties of proteins.
  • Utilized known universalities in the spatial organization of soluble proteins.
  • Developed and validated the D2N metric.

Main Results:

  • The D2N metric accurately predicts the RMSD of protein structures.
  • Achieved a prediction error of ±1.5 Å.
  • Demonstrated remarkable average accuracy of 93.6% for structures within 5 Å of the native structure.
  • The D2N tool is available online for public use.

Conclusions:

  • The D2N metric offers a reliable way to assess protein structure quality computationally.
  • This method opens new possibilities for assigning structures to entire proteomes, even without experimental data.
  • Facilitates advancements in structural bioinformatics and computational biology research.