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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...
Improving Translational Accuracy02:07

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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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Conservation of Protein Domains Over Different Proteins

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Published on: July 14, 2015

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments.

Michael L Sierk1, Michael E Smoot, Ellen J Bass

  • 1Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

BMC Bioinformatics
|March 24, 2010
PubMed
Summary
This summary is machine-generated.

Suboptimal protein sequence alignments can accurately reflect structural alignments. A new regression model improves protein alignment accuracy by analyzing suboptimal alignments, enhancing the discovery of homologous proteins.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Pairwise sequence alignments are crucial for identifying homologous proteins.
  • However, sequence alignments often fail to accurately represent structural alignments derived from 3D coordinates.
  • Suboptimal sequence alignments may better reflect structural information.

Purpose of the Study:

  • To investigate the relationship between suboptimal sequence alignments and structural alignments.
  • To develop a method for improving the accuracy of pairwise protein sequence alignments.
  • To identify which sequence alignments are most likely to be structurally accurate.

Main Methods:

  • Compared near-optimal and probabilistic sequence alignments with structure-based alignments.
  • Developed a logistic regression model using alignment features (robustness, edge frequency, max bits-per-position).
  • Evaluated model performance using ROC analysis and tested various trimming protocols.

Main Results:

  • Significant overlap exists between structural alignments and near-optimal/probabilistic sequence alignments for similar sequences (E-values < 10-5).
  • The logistic regression model accurately classifies amino acid pairs for structural alignment likelihood.
  • Trimming protocols and model-generated probabilities improve alignment accuracy, with novel correct structural edges identified.

Conclusions:

  • Suboptimal pairwise protein sequence alignments show substantial overlap with structure-based alignments for statistically significant similarities.
  • A regression model utilizing information from suboptimal alignments enhances the accuracy of pairwise alignments relative to structure-based alignments.