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Related Concept Videos

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...
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...

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Related Experiment Video

Updated: May 11, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

New model-fitting and model-completion programs for automated iterative nucleic acid refinement.

Keitaro Yamashita1, Yong Zhou, Isao Tanaka

  • 1Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.

Acta Crystallographica. Section D, Biological Crystallography
|May 23, 2013
PubMed
Summary
This summary is machine-generated.

New software, NAFIT and NABUILD, aids in analyzing nucleic acid structures from X-ray crystallography. These tools improve electron density fitting and model building, enhancing the understanding of DNA and RNA biological functions.

Keywords:
LAFIREautomatic refinementnucleic acid model buildingnucleic acid model fittingreal-space refinement

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Determining nucleic acid structures is crucial for understanding biological functions.
  • Poor X-ray diffraction from nucleic acid crystals complicates electron-density interpretation.
  • Crystallographic expertise and knowledge of nucleic acid structure are essential for model building.

Purpose of the Study:

  • To introduce NAFIT and NABUILD, novel software programs for fitting and extending nucleic acid models.
  • To provide tools that can be used independently or integrated into automated refinement systems like LAFIRE.
  • To address the challenges in electron-density interpretation for nucleic acid crystallography.

Main Methods:

  • NAFIT utilizes sequential grouped fitting with empirical torsion-angle and antibumping restraints, including hydrogen atoms.
  • NABUILD employs a coarse-grained approach using a skeletonized map to extend nucleic acid models.
  • The programs are designed for both automated and independent use in structural analysis.

Main Results:

  • NAFIT significantly enhances electron-density fit and improves the geometric quality of nucleic acid models.
  • Iterative refinement incorporating NABUILD leads to a substantial reduction in the Rfree factor.
  • The software facilitates more accurate and efficient determination of nucleic acid structures.

Conclusions:

  • NAFIT and NABUILD offer valuable advancements for nucleic acid structure determination.
  • These programs improve the accuracy and efficiency of crystallographic model building.
  • The developed tools contribute to a deeper understanding of nucleic acid biological roles.