PocketMatch: A new algorithm to compare binding sites in protein structures
2008
PocketMatch: A New Algorithm for Comparing Protein Binding Sites
Sample size: 20000
publication
Evidence: high
Author Information
Author(s): Yeturu Kalidas, Chandra Nagasuma
Primary Institution: Indian Institute of Science, Bangalore
Hypothesis
Can a new algorithm improve the comparison of protein binding sites with high sensitivity?
Conclusion
The PocketMatch algorithm allows for accurate and efficient comparison of protein binding sites.
Supporting Evidence
- PocketMatch was validated against known binding site similarities.
- The algorithm demonstrated high sensitivity to minor perturbations in binding site geometry.
- It effectively discriminated between similar and dissimilar binding sites.
Takeaway
Scientists created a new tool called PocketMatch to help compare parts of proteins that bind to other molecules, making it easier to find similarities.
Methodology
The algorithm represents binding sites as sorted lists of distances and uses an alignment method to compare them.
Limitations
The representation is conceptually simplistic and may not capture all nuances of binding site similarities.
Digital Object Identifier (DOI)
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