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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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Improving your target-template alignment with MODalign.

Alessandro Barbato1, Pascal Benkert, Torsten Schwede

  • 1Department of Physics, Sapienza University P.le A. Moro, 5, 00185 Rome, Italy.

Bioinformatics (Oxford, England)
|February 7, 2012
PubMed
Summary
This summary is machine-generated.

MODalign is a web tool that helps protein modelers manually adjust sequence alignments. It updates related biological data, simplifying protein structure modeling and analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein structure modeling relies heavily on accurate sequence alignments between target proteins and their templates.
  • Manual inspection and modification of these alignments are crucial but can be complex and time-consuming.

Purpose of the Study:

  • To introduce MODalign, an interactive web-based tool designed to assist protein structure modelers.
  • To streamline the process of inspecting and manually modifying target-template sequence alignments.

Main Methods:

  • MODalign interactively computes and displays multiple sequence alignments, conservation scores, secondary structure, solvent accessibility, and local quality scores.
  • The tool updates these biological data points in real-time upon modification of the target-template alignment.

Main Results:

  • MODalign provides an integrated environment for visualizing and refining sequence alignments within the context of protein structure information.
  • The tool facilitates the assessment of alignment quality and its impact on downstream modeling steps.

Conclusions:

  • MODalign simplifies the critical target-template alignment step in protein structure modeling.
  • The tool is versatile, applicable to any scenario requiring sequence alignment inspection alongside related biological data.