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Related Concept Videos

Protein Folding01:22

Protein Folding

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Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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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.
The primary structure of a protein is its amino acid sequence.
Lattice Centering and Coordination Number02:33

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The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
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Related Experiment Video

Updated: Jun 19, 2026

Fabrication of Three-Dimensional Graphene-Based Polyhedrons via Origami-Like Self-Folding
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RNA folding on the 3D triangular lattice.

Joel Gillespie1, Martin Mayne, Minghui Jiang

  • 1Department of Computer Science, Utah State University, Logan, Utah 84322-4205, USA. jgillespie@cc.usu.edu

BMC Bioinformatics
|November 7, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a novel 3D triangular lattice model for RNA folding simulation, improving RNA secondary structure prediction accuracy, including pseudoknots. The method outperforms existing algorithms and offers reconstruction capabilities.

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Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Biophysics

Background:

  • Lattice models are crucial for studying complex biological problems like protein and RNA folding.
  • Understanding RNA folding dynamics is essential for predicting its structure and function.

Purpose of the Study:

  • To develop and evaluate a novel method for predicting RNA secondary structures, including pseudoknots, using 3D triangular lattice folding simulations.
  • To create an efficient reconstruction method for RNA secondary structure prediction.

Main Methods:

  • Simulating RNA folding dynamics on a 3D triangular lattice.
  • Extracting and selecting disjoint base pairs from optimal lattice conformations.
  • Implementing computer programs for simulation and visualization of RNA folding.

Main Results:

  • The novel method demonstrates superior performance compared to the HotKnot algorithm for RNA pseudoknot prediction.
  • The method is adaptable for reconstructing RNA conformations from secondary structures.
  • Developed software for simulation and visualization of RNA folding on the 3D triangular lattice.

Conclusions:

  • 3D triangular lattice folding simulation is an effective approach for RNA secondary structure prediction and conformation reconstruction.
  • The visualization software serves as a valuable tool for RNA folding research and education.