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Updated: May 24, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Evolutionary inaccuracy of pairwise structural alignments.

M I Sadowski¹, W R Taylor

¹Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK.

Bioinformatics (Oxford, England)

|March 9, 2012

Summary

This summary is machine-generated.

Assessing structural alignment consistency reveals significant variability among methods. Even for similar proteins, alignments show high inconsistency, highlighting room for improvement in protein structure analysis tools.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Area of Science:

Bioinformatics
Structural Biology
Computational Biology

Background:

Structural alignment methods are crucial for protein analysis, but their accuracy is hard to verify due to unknown evolutionary histories.
Assessing alignment consistency offers an objective measure of quality and identifies areas for method enhancement.

Purpose of the Study:

To evaluate the self-consistency of seven prominent structural alignment methods.
To identify factors contributing to inconsistencies in structural alignments.
To assess the performance of these methods using geometric measures.

Main Methods:

Analyzed self-consistency of SAP, TM-align, Fr-TM-align, MAMMOTH, DALI, CE, and FATCAT.
Used a non-redundant dataset of 1863 protein domains from the SCOP database.
Assessed alignment quality using geometric measures.

Main Results:

High residue-level inconsistency (30%) was observed even for similar proteins across seven structural alignment methods.
SAP and Fr-TM-align demonstrated higher consistency compared to other methods.
Inconsistencies were more prevalent near gaps, in proteins with low structural complexity, and within helical regions.
FATCAT (flexible mode) excelled in identifying good structural alignments via geometric measures despite its inconsistency.

Conclusions:

Significant scope exists for enhancing the consistency of current structural alignment algorithms.
Understanding inconsistency sources can guide the development of more reliable protein structure alignment tools.