Please cite PDBeFold for all results obtained from this service, should
these results be published in any form or otherwise presented.
PDBeFold should be referenced to as
Protein structure comparison service PDBeFold at European
authored by E. Krissinel and K. Henrick
citing the following:
E. Krissinel and K. Henrick (2004).
Secondary-structure matching (SSM), a new tool for fast protein
structure alignment in three dimensions
Acta Cryst. D60, 2256---2268
The algorithm of multiple structure alignment, used in PDBeFold,
is described in the following publication:
E. Krissinel and K. Henrick (2005).
Multiple Alignment of Protein Structures in Three Dimensions
In: M.R. Berthold et.al.
CompLife 2005, LNBI 3695, pp. 67--78
Springer-Verlag Berlin Heidelberg.
PDBeFold is based on the original algorithm of graph matching.
A detail description of the algorithm is published in the following
reference (the downloadable document exemplifies
the submitted paper; the published one differs by layout and minor
E. Krissinel and K. Henrick (2004). Common subgraph isomorphism
detection by backtracking search
Software: Practice and Experience, 34, Iss. 6, p.591-607
The design concept and programming technology, used in PDBeFold, are based on
the new CCP4 Coordinate Library
E. B. Krissinel, M. D. Winn, C. C. Ballard, A. W. Ashton, P. Patel,
E. A. Potterton, S. J. McNicholas, K. D. Cowtan and P. Emsley (2004).
The new CCP4 Coordinate Library as a toolkit for the design
of coordinate-related applications in protein crystallography
Acta Cryst. D60, 2250---2255
PDBeFold has been presented on international forums:
E. Krissinel and K. Henrick (2003). Protein structure comparison in 3D
based on secondary structure matching (PDBeFold) followed by
Ca alignment, scored by a new structural
. In: Andreas J. Kungl & Penelope
J. Kungl (Eds.), Proceedings of the
5th International Conference on Molecular Structural Biology
Vienna, September 3-7, 2003, p.88.
The following publication exemplifies our own research using
E. Krissinel (2007). On the relationship between sequence and structure
similarities in proteomics
Bioinformatics 23, 717---723