SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

Area of Science:

• Bioinformatics
• Computational Biology
• Structural Bioinformatics

Background:

• Accurate protein sequence alignment is critical for homology modeling and active site prediction.
• Alignment errors often lead to low-quality protein structure models.
• There is a need for bioinformatics tools to enhance protein alignment accuracy.

Purpose of the Study:

• To develop a web-based tool, SFESA, for refining pairwise protein sequence alignments.
• To improve the accuracy of protein sequence alignments beyond current advanced methods.

Main Methods:

• SFESA refines pairwise protein sequence alignments by searching for homologs with available 3D structures to use as templates.
• It evaluates alignment variants based on local shifts of secondary structure elements.
• A scoring function combining sequence and structure-based scores is employed.

Main Results:

• SFESA refines pairwise protein sequence alignments more accurately than existing advanced methods like HHpred and CNFpred.
• The tool improves alignments generated by other software.
• SFESA utilizes a combined sequence and structure scoring approach for alignment blocks.

Conclusions:

• SFESA is a unique web server that refines protein alignments by assessing local shifts in secondary structure elements.
• It offers researchers a tool to compute, refine, and evaluate pairwise alignments.
• The SFESA web server is accessible at http://prodata.swmed.edu/sfesa.