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Updated: Aug 1, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
STRAP: editor for STRuctural Alignments of Proteins
1Institute of Biochemistry, Charité, Medical Faculty of the Humboldt University, Monbijoustrasse 2a, 10117 Berlin, Germany.
STRAP is a user-friendly tool for protein sequence alignment, incorporating structural data for improved accuracy. It efficiently manages large datasets and integrates with popular protein viewers.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Bioinformatics
Background:
- Multiple sequence alignment is crucial for understanding protein function and evolution.
- Integrating structural information can enhance alignment accuracy, especially for distantly related proteins.
- Existing tools may lack user-friendliness or efficient handling of large datasets.
Purpose of the Study:
- To introduce STRAP, a novel tool for generating and refining protein sequence alignments.
- To highlight STRAP's unique feature of visualizing spatial distances for incorporating structural information.
- To demonstrate STRAP's capability in managing large-scale alignments and its extensibility.
Main Methods:
- STRAP supports multiple input file formats (SwissProt, GenBank, EMBL, DSSP, PDB, MSF, ASCII).
- It features a unique visualization of C(alpha)-atom spatial distances within the alignment.
- STRAP embeds protein viewers (INSIGHT, RASMOL, WEBMOL) and is written in JAVA.
Main Results:
- STRAP provides a comfortable and extensible platform for protein sequence alignment.
- The spatial distance visualization aids in incorporating structural information, guiding alignment for low similarity sequences.
- The tool efficiently manages large alignments and integrates with external visualization software.
Conclusions:
- STRAP offers a valuable, user-friendly approach to protein sequence alignment by integrating structural data.
- Its design facilitates easy adaptation and potential development into more complex alignment tools.
- STRAP enhances the process of multiple sequence alignment, particularly for challenging datasets.
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