ProCKSI

= Further Literature =

ProCKSI: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures[[br]]

D. Barthel, J. D. Hirst, J. Blazewicz and N. Krasnogor, Late-Breaking Results, ''5th European Conference on Computational Biology (ECCB06)'', Israel, 2007.

[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric][[br]]

N. Krasnogor and D. A. Pelta. ''Bioinformatics'' 20(7), 1015-1021, 2004.

[http://www.sciencedirect.com/science/article/B6V05-4DV1959-2/2/aabb4b5cb25dabb343c6d7f7109aa615 A fuzzy sets based generalization of contact maps for the overlap of protein structures][[br]]

D. A. Pelta, N. Krasnogor, C. Bousono-Calzon, J. L. Verdegay, J. D. Hirst and E. Burke. ''Fuzzy Sets and Systems'' 152(1), 101-123, 2005.

[http://www.liebertonline.com/doi/abs/10.1089/106652704773416876 1001 optimal PDB structure alignments: Integer Programming methods for finding the maximum contact map overlap][[br]]

A. Caprara, G. Lancia, B. Carr, B. Walenz and S. Istrail, ''Journal of Computational Biology'' 11(1), 27-52, 2004.

[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/6/566 DaliLite workbench for protein structure comparison][[br]]

L. Holm and J. Park, <i>Bioinformatics</i> 16, 566-567, 2000.

[http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html A Gene Network for Navigating the Literature][[br]]

R. Hoffmann and A. Valencia, ''Nature Genetics'' 36, 664-664, 2004.

[http://protein.oupjournals.org/cgi/content/abstract/11/9/739 Protein structure alignment by incremental combinatorial extension (CE) of the optimal path][[br]]

I. N. Shindyalov and P. E. Bourne, ''Protein Engineering'' 11, 739-747, 1998.

[http://nar.oxfordjournals.org/cgi/content/abstract/33/7/2302 TM-align: A protein structure alignment algorithm based on TM-score][[br]]

Y. Zhang and J. Skolnick, ''Nucleic Acids Research'' 33, 2302-2309, 2005.

[http://doi.wiley.com/10.1002/prot.20331 FAST: A Novel Protein Structure Alignment Algorithm][[br]]

J. Zhu and Y. Weng, <i>Proteins: Structure, Function and Bioinformatics</i> 14, 417-423, 2005.

[http://doi.wiley.com/10.1002/prot.20331 Vorolign - Fast Structural Alignment using Voronoi Contacts][[br]]

F. Birzele, J. E. Gewehr, G. Csaba and R. Zimmer, ''Bioinformatics'' 23, e205-e211, 2007.

[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric][[br]]

N. Krasnogor and D. A. Pelta. ''Bioinformatics'' 20(7), 1015-1021, 2004.

[http://www.cs.nott.ac.uk/~nxk/PAPERS/s112-01.pdf Selecting protein fuzzy contact maps through information and structure measures][[br]]

C. Bousono-Calzon, A. Oropesa-Garcia and N. Krasnogor. Proceedings of the ''Fourth Conference of the European Society for Fuzzy Logic and Technology and 11 Recontres Francophones sur la Logique Floue et ses Applications (EUSFLAT-LFA, 2005)'', pp 1106-1111, 2005.

[http://www.cs.nott.ac.uk/~nxk/PAPERS/s112-04.pdf Protein Structure Comparison through Fuzzy Contact Maps and the Universal Similarity Metric][[br]]

D. A. Pelta, J. R. Gonzales and N. Krasnogor. Proceedings of the ''Fourth Conference of the European Society for Fuzzy Logic and Technology and 11 Recontres Francophones sur la Logique Floue et ses Applications (EUSFLAT-LFA, 2005)'', 1124-1129, 2005.

[http://www.sciencemag.org/cgi/content/abstract/273/5275/595 Mapping the protein universe][[br]]

Holm L. and Sander C., ''Science'' 273, 595-602, 1996.

[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&dopt=Citation&list_uids=8377180 Protein Structure Comparison by Alignment of Distance Matrices][[br]]

L. Holm and C. Sander, ''J. Mol. Biol.'' 223, 123-138, 1993.

[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/suppl_2/ii252?etoc Implementing the iHOP concept for navigation of biomedical literature][[br]]

R. Hoffmann, and A. Valencia, ''Bioinformatics'' 21, ii252-ii258, 2005.

[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/7/660 Visualizing large hierarchical clusters in hyperbolic space][[br]]

J. Bingham, S. Sudarsanam, ''Bioinformatics'' 16(7), 660-661, 2000.

MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures[[br]]

Per J. Kraulis, J. Appl. Cryst. 24, 946-950, 1991.

Raster3D: photorealistic molecular images[[br]]

E.A. Merritt, D.J. Bacon, ''Meth. Enzymol.'' 277, 505-524, 1997.

[http://nar.oxfordjournals.org/cgi/content/abstract/28/1/235 The Protein Data Bank][[br]]

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, P. Bourne, Nucleic Acids Res. 28, 235–242, 2000.