RAPIDO: A New Method for Protein Structure Alignment
Author Information
Author(s): Roberto Mosca, Barbara Brannetti, Thomas R. Schneider
Primary Institution: IFOM, the FIRC Institute for Molecular Oncology Foundation
Hypothesis
Can a new algorithm improve the alignment of protein structures that undergo conformational changes?
Conclusion
RAPIDO is more sensitive than other flexible aligners and can detect similarities in closely homologous proteins undergoing large conformational changes.
Supporting Evidence
- RAPIDO can align protein structures with large conformational changes effectively.
- The algorithm identifies structurally conserved regions even when they are not continuous in sequence.
- RAPIDO's results are consistent with manual analyses in the literature.
Takeaway
RAPIDO helps scientists compare proteins even when they change shape, making it easier to find similarities between them.
Methodology
The RAPIDO algorithm uses a genetic algorithm to align protein structures while accounting for flexibility and conformational changes.
Limitations
RAPIDO may produce shorter alignments for distantly related structures and can sometimes misalign fragments that are locally similar but not equivalent.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website