Bioinformatics, Vol 14, 295-308, Copyright © 1998 by Oxford University Press
R Zimmer, M Wohler and R Thiele
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.
AVAILABILITY: The potentials are made available via the program system
ToPLign (URL: http://cartan.gmd.de/ToPLign.html). CONTACT:
Ralf.Zimmer,Ralf.Thiele@gmd.de
ARTICLES
New scoring schemes for protein fold recognition based on Voronoi contacts
Institute for Algorithms and Scientific Computing (SCAI), German National Research Center for Information Technology (GMD), 53754 Sankt Augustin, Germany.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  F. Birzele, J. E. Gewehr, G. Csaba, and R. Zimmer Vorolign--fast structural alignment using Voronoi contacts Bioinformatics, January 15, 2007; 23(2): e205 - e211. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. P. Gore, D. F. Burke, and T. L. Blundell PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes Bioinformatics, August 1, 2005; 21(15): 3316 - 3317. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. de Vries, R. M.A. Knegtel, E. H. Holmes, and B. A. Macher Fucosyltransferases: structure/function studies Glycobiology, October 1, 2001; 11(10): 119R - 128R. [Abstract] [Full Text] [PDF]
|
|