TY  - JOUR
U1  - Zeitschriftenartikel, wissenschaftlich - begutachtet (reviewed)
A1  - Zimmer, Ralf
A1  - Wöhler, Marko
A1  - Thiele, Ralf
T1  - New scoring schemes for protein fold recognition based on Voronoi contacts
JF  - Bioinformatics
N2  - MOTIVATION: 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.
SN  - 1367-4803
SS  - 1367-4803
U6  - https://doi.org/10.1093/bioinformatics/14.3.295
DO  - https://doi.org/10.1093/bioinformatics/14.3.295
PM  - 9614274
VL  - 14
IS  - 3
SP  - 295
EP  - 308
PB  - Oxford University Press
ER  -