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Related Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Related Experiment Video

Updated: Jul 11, 2026

Three-Dimensional Shape Modeling and Analysis of Brain Structures
05:33

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Published on: November 14, 2019

High accuracy template based modeling by global optimization.

Keehyoung Joo1, Jinwoo Lee, Sunjoong Lee

  • 1School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.

Proteins
|September 27, 2007
PubMed
Summary

This study presents an optimized template-based modeling procedure for protein structure prediction. Rigorous optimization of scoring functions significantly improved backbone and side-chain modeling accuracy for CASP7 targets.

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

Published on: July 25, 2013

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Last Updated: Jul 11, 2026

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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:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Template-based modeling (TBM) is a key approach for protein structure prediction.
  • High accuracy in TBM requires effective optimization of scoring functions at multiple stages.
  • CASP7 targets present challenges for accurate protein structure modeling.

Purpose of the Study:

  • To develop and apply a rigorous optimization procedure for high-accuracy template-based modeling.
  • To enhance the accuracy of both backbone and side-chain modeling in protein structure prediction.
  • To evaluate the performance of the optimized method on CASP7 targets.

Main Methods:

  • Applied a procedure based on rigorous optimization of score functions at three stages: multiple alignment, chain building, and side-chain modeling.
  • Utilized conformational space annealing with a new consistency-based score function for multiple alignment.
  • Optimized the MODELLER energy function for chain building and a SCWRL-like energy function with a target-specific rotamer library for side-chain modeling.

Main Results:

  • Achieved significant improvements in backbone and side-chain modeling accuracy for TBM and TBM/HA targets.
  • For most TBM/HA targets (17/26), the predicted model surpassed models built from the best template post-hoc.
  • Demonstrated the method's capability to extract relevant information from multiple templates.

Conclusions:

  • The rigorous optimization procedure significantly enhances template-based protein modeling accuracy.
  • The developed method shows potential for extracting valuable information from multiple templates for improved structure prediction.
  • This approach offers a robust strategy for high-accuracy modeling of challenging protein targets.