Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration

Keim, Daniel A.; Oelke, Daniela; Truman, Royal; Neuhaus, Klaus

Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration

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Date

2006

Authors

Keim, Daniel A.

Oelke, Daniela

Truman, Royal

Neuhaus, Klaus

DOI (citable link)

10.1109/BIBE.2006.253333

Collections

Informatik und Informationswissenschaft

Publication type

Contribution to a conference collection

Publication status

Published

Published in

Proceedings : Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006, 16-18 October 2006, Arlington, Virginia. - Los Alamitos, California : IEEE, 2006. - pp. 183-192. - ISBN 0-7695-2727-2

Abstract

The analysis of alignments of functionally equivalent proteins can reveal regularities such as correlated positions or residue patterns which are important to ensure a specific fold and various cellular functions. Many approaches are found in the literature which try to identify correlated positions to predict the residues that are close to each other in the three-dimensional folded structure. However, the quality of the predictions remains disappointing. One of the problems is that the statistical correlation measures that were used cannot do justice to the underlying complex biological and physicochemical realities. In this paper we evaluate the biological requirements for a correlation measure and explain why a completely automatic approach is unlikely to succeed. We then propose a novel and flexible criteria for correlation of residue positions in protein sequences, which can be optimized for different requirements. To apply this definition we developed the tool VisAlign that combines an automatic calculation of correlations with an interactive visualization. This allows the user to visually explore alternative alignments and thereby conveniently test various hypothesis and to detect regularities in the aligned sequences

Subject (DDC)

004 Computer Science

Conference

BIBE 2006, Oct 16, 2006 - Oct 18, 2006, Arlington, VA, USA

Cite This

ISO 690

KEIM, Daniel A., Daniela OELKE, Royal TRUMAN, Klaus NEUHAUS, 2006. Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration. BIBE 2006. Arlington, VA, USA, Oct 16, 2006 - Oct 18, 2006. In: Proceedings : Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006, 16-18 October 2006, Arlington, Virginia. Los Alamitos, California:IEEE, pp. 183-192. ISBN 0-7695-2727-2. Available under: doi: 10.1109/BIBE.2006.253333

BibTex

@inproceedings{Keim2006-10Findi-40814,
  year={2006},
  doi={10.1109/BIBE.2006.253333},
  title={Finding Correlations in Functionally Equivalent Proteins by Integrating Automated and Visual Data Exploration},
  isbn={0-7695-2727-2},
  publisher={IEEE},
  address={Los Alamitos, California},
  booktitle={Proceedings : Sixth IEEE Symposium on BioInformatics and BioEngineering, BIBE 2006, 16-18 October 2006, Arlington, Virginia},
  pages={183--192},
  author={Keim, Daniel A. and Oelke, Daniela and Truman, Royal and Neuhaus, Klaus}
}

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Bibliography of Konstanz

Yes