Towards Optimal Views of Proteins

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.

[1]  Maccallum Rm.  Computational analysis of protein sequence and structure. , 1997 .

[2]  W G Richards,et al.  A novel representation of protein structure. , 1995, Journal of molecular graphics.

[3]  R. Pickersgill,et al.  High resolution structure and sequence of T. aurantiacus Xylanase I: Implications for the evolution of thermostability in family 10 xylanases and enzymes with βα‐barrel architecture , 1999 .

[4]  T. P. Flores,et al.  An algorithm for automatically generating protein topology cartoons. , 1994, Protein engineering.

[5]  R. Pickersgill,et al.  High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture. , 1999, Proteins.

[6]  T. P. Flores,et al.  Protein structural topology: Automated analysis and diagrammatic representation , 2008, Protein science : a publication of the Protein Society.

[7]  Patrice Koehl,et al.  The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..

[8]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[9]  C. Chothia,et al.  Structural patterns in globular proteins , 1976, Nature.

[10]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[11]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[12]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[13]  Anne Lecroisey,et al.  The crystal structure of HasA, a hemophore secreted by Serratia marcescens , 1999, Nature Structural Biology.

[14]  Teuvo Kohonen,et al.  Self-organized formation of topologically correct feature maps , 2004, Biological Cybernetics.