Similarity search for local protein structures at atomic resolution by exploiting a database management system

@inproceedings{Kinjo2007SimilaritySF,
  title={Similarity search for local protein structures at atomic resolution by exploiting a database management system},
  author={Akira R. Kinjo and Haruki Nakamura},
  booktitle={Biophysics},
  year={2007}
}
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational database management system with appropriate indexing of geometric data. This method, which we call geometric indexing, can enumerate ligand binding sites that are structurally similar to sub-structures of a query protein among more than 160,000 possible… CONTINUE READING
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