New scoring schemes for protein fold recognition based on Voronoi contacts.
BACKGROUND
The genome projects produce a wealth of protein sequences. Theoretical methods to predict possible structures and functions are needed for screening purposes, large-scale comparisons and in-depth analysis to identify worthwhile targets for further experimental research. Sequence-structure alignment is a basic tool for the identification of model folds for protein sequences and the construction of crude structural models. Empirical contact potentials (potentials of mean force) are used to optimize and evaluate such alignments.


RESULTS
We propose new scoring schemes based on a contact definition derived from Voronoi decompositions of the three-dimensional coordinates of protein structures. We demonstrate that Voronoi potentials are superior to pure distance-based contact potentials with respect to recognition rate and significance for native folds. Moreover, the scoring scheme has the potential to provide a reasonable balance of detail and ion such that it is also useful for the recognition of distantly related (both homologous and non-homologous) proteins. This is demonstrated here on a set of structural alignments showing much better correspondence of native and model scores for the Voronoi potentials as compared to conventional distance-based potentials.


BACKGROUND
The potentials are made available via the program system ToPLign (URL: http://cartan.gmd.de/ToPLign.html).


BACKGROUND
Ralf.Zimmer,Ralf.Thiele@gmd.de
Zimmer
R
R
Institute for Algorithms and Scientific Computing (SCAI), German National Research Center for Information Technology (GMD), 53754 Sankt Augustin, Germany.
Wöhler
M
M
Thiele
R
R
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D008954:Models, Biological; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D017421:Sequence Analysis / Q000379:methods*; D012986:Software Validation
D000596:Amino Acids