Towards optimal views of proteins.
BACKGROUND
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.


BACKGROUND
The source code is available from the OVOP homepage: http://www.sbc.su.se/~oscar/ovop.
Sverud
Oscar
O
Stockholm Bioinformatics Center, Stockholm University, Sweden.
MacCallum
Robert M
RM
D000465:Algorithms; D003196:Computer Graphics; D003628:Database Management Systems; D030562:Databases, Protein; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008958:Models, Molecular; D016571:Neural Networks, Computer; D015588:Observer Variation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011786:Quality Control; D012399:Rotation; D013205:Staphylococcal Protein A / Q000737:chemistry; D011795:Surveys and Questionnaires; D014584:User-Computer Interface
D011506:Proteins; D013205:Staphylococcal Protein A