SURF

Gabrielle Ho

Enriching the SCOP Database with Phylogenetic and Protein Function Data

Different protein databases classify and organize proteins based on separate criteria. As a result, the organization and information available on these databases will often vary. By mapping the protein domains between different databases, I can analyze and add new, otherwise not apparent information. During the summer, I am augmenting the computational resources available on the Structural Classification of Proteins (SCOP) database by mapping it to the Uniprot Gene Ontology Annotation Database (Uniprot-GOA) and the Pfam Database. Based on the results of mapping the Pfam database to SCOP, I can uncover the internal phylogeny of SCOP families and organize new protein sequences within SCOP without necessarily knowing the structures. The Uniprot-GOA mapping will be used to assign protein functions to the Protein Data Bank entries in SCOP and improve the search function to include GO annotations.

Message to Sponsor

The SURF/Rose Hills program really gives me an opportunity to devote my summer to experiencing full time research. I am very grateful to the sponsors and the Brenner lab for giving me the time and resources to help me develop my experience and skills in both programming and biology. I would not have been able to have the chance to be involved in contributing to the field of computational biology without everyones support. Thank you to the foundation for making this possible!
  • Major: Molecular and Cell Biology, Computer Science (minor)
  • Sponsor: Rose Hills Foundation
  • Mentor: Steven Brenner, Plant and Microbial Biology