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Related Concept Videos

DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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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Updated: Jun 22, 2026

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

A guide to template based structure prediction.

Xiaotao Qu1, Rosemarie Swanson, Ryan Day

  • 1Moffitt Cancer Center, Tampa, FL 33612, USA.

Current Protein & Peptide Science
|June 13, 2009
PubMed
Summary
This summary is machine-generated.

Template-based protein structure prediction leverages known structures to model new ones. However, starting near the native structure presents challenges, limiting progress in this field.

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Last Updated: Jun 22, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

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Published on: November 3, 2011

The ITS2 Database
16:17

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Published on: March 12, 2012

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Template-based protein structure prediction, also known as homology or comparative modeling, utilizes existing solved protein structures to predict the three-dimensional fold of a target protein sequence.
  • This method relies on the principles that similar sequences adopt similar folds and that a significant portion of protein fold space is represented in the Protein Data Bank (PDB).

Purpose of the Study:

  • To provide a comprehensive review of template-based protein structure prediction methods.
  • To outline the general concepts, procedures, and established software involved in this prediction technique.
  • To discuss the limitations and challenges, particularly those arising from the method's proximity to the native structure, and to identify areas for future improvement.

Main Methods:

  • The review covers key steps including sequence alignment, parent structure selection, template structure building, refinement (backbone moves, side-chain packing, loop modeling), and evaluation.
  • Established software and algorithms are described, with their respective advantages and limitations analyzed.
  • Developments up to the 7th Critical Assessment of Structure Prediction meeting are discussed.

Main Results:

  • Template-based modeling aims for atomically accurate models by mapping target sequences onto homologous parent structures.
  • The inherent assumption of proximity to the native structure, while promising, is identified as a primary obstacle to significant progress.
  • Established methods and software exist, but their effectiveness is constrained by the starting point of the prediction.

Conclusions:

  • Template-based protein structure prediction is a valuable tool but faces inherent difficulties due to its reliance on templates close to the native structure.
  • Further advancements are needed to overcome these limitations and improve the accuracy and scope of homology modeling.
  • Understanding the challenges associated with refining models that begin near the native conformation is crucial for future developments in the field.