Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature

Multiple Sequence Alignment

Abstract

Protein structure visualization tools render images that allow the user to explore structural features of a protein. Context specific information relating to a particular protein or protein family is not easily integrated and must be uploaded from databases or provided through manual curation of input files. We describe a mixed natural language processing and sequence analysis based approach for the retrieval of mutation specific annotations from full text articles for rendering with protein structures.

Keywords

Text Mining, Protein Structure Annotation, Protein Function, ProSAT, Xylanase

Reference

Christopher J. O. Baker and René Witte, Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature. The Third Canadian Working Conference on Computational Biology (CCCB'04), October 4th, 2004, Markham, Ontario, Canada.

Bibtex entry (also for download):

@InProceedings{cbrw04,
  author = 	 {Christopher J.O. Baker and Ren\'{e} Witte},
  title = 	 {{Enriching Protein Structure Visualizations with Mutation Annotations 
                 Obtained by Text Mining Protein Engineering Literature}},
  booktitle =	 {The 3rd Canadian Working Conference on Computational Biology (CCCB'04)},
  year =	 {2004},
  address =	 {Markham, Ontario, Canada},
  month =	 {October 4},
  note =	 {Co-located with IBM CASCON.}
}

You can also visit the conference website and IBM's CASCON page for the workshop.

Software

For downloading our open source software, please refer to the successor project, Open Mutation Miner (OMM).

Download

Download the full CCCB'04 workshop report: IBM Technical Report TR-74-203-8
Only the paper (local copy): baker_witte_cccb04.pdf.
MD5 checksum: 334148612ce1e09a12de3f1ed3b30221

Copyright © 2004 Christopher Baker and René Witte.