PDBeFold Citation

 

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 Bioinformatics Institute
(http://www.ebi.ac.uk/msd-srv/ssm), 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. (Eds.): 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 corrections):

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 similarity function. 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 PDBeFold:

E. Krissinel (2007). On the relationship between sequence and structure similarities in proteomics. Bioinformatics 23, 717---723