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Bioinformatics Vol. 19 no. 7 2003
Pages 882-888
© 2003 Oxford University Press

Towards optimal views of proteins

Oscar Sverud and Robert M. MacCallum *

Stockholm Bioinformatics Center, Stockholm University, 106 91 Stockholm, Sweden

Received on August 15, 2002 ; revised on October 23, 2002 and December 17, 2002 ; accepted on December 19, 2002

Motivation: Graphical representations of proteins in online databases generally give default views orthogonal to the PDB file coordinate system. These views are often uninformative in terms of protein structure and/or function. Here we discuss the development of a simple automatic algorithm to provide a ‘good’ view of a protein domain with respect to its structural features.

Results: We used dimension reduction with the preservation of topology (using Kohonen’s self organising map) to map 3D carbon alpha coordinates into 2D. The original protein structure was then rotated to the view which corresponded most closely to the 2D mapping. This procedure, which we call OVOP, was evaluated in a public blind trial on the web against random views and a ‘flattest’ view. The OVOP views were consistently rated ‘better’ than the other views by our volunteers.

Availability: The source code is available from the OVOP homepage: http://www.sbc.su.se/~oscar/ovop

Contact: maccallr{at}sbc.su.se

* To whom correspondence should be addressed.


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