ProCKSI

= Further Literature =

2008
D.A. Pelta, J.R. Gonzalez, and M. Moreno Vegabr
'''A simple and fast heuristic for protein structure comparison'''br
''BMC Bioinformatics'', 2008 (to appear)

A.A. Shah, D. Barthel, P. Łukasiak, J. Błażewicz, and N. Krasnogor ([http://www.ingentaconnect.com/search/article?title=web+and+grid&title_type=tka&author=Krasnogor&journal=current+bioinformatics&journal_type=words&volume=3&issue=1&year_from=2003&year_to=2008&database=1&pageSize=20&index=1 publisher])br
'''Web & Grid Technologies in Bioinformatics, Computational Biology and Systems Biology: A Review.''' br
''Current Bioinformatics'', 3, 10-31, 2008.

2007
D. Barthel, J.D. Hirst, J. Błażewicz, E.K. Burke, and N. Krasnogor ([http://www.biomedcentral.com/1471-2105/8/416/abstract publisher])br
'''The ProCKSI Server: A Decision Support System for Protein (Structure) Comparison, Knowledge, Similarity and Information.''' br
''BMC Bioinformatics'' 2007, 8, 416.

A.A. Shah, D. Barthel, and N. Krasnogor ([http://www.springerlink.com/content/90n46423p200502r/ publisher], [http://dblp.uni-trier.de/rec/bibtex/conf/ispa/ShahBK07 bibtex])br
'''Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overview.'''br
In P. Thulasiraman, X. He, T. Li-Xu, M. Denko, R.K. Thulasiram, and L.T. Yang (Eds.), ''Frontiers of High Performance Computing and Networking ISPA 2007 Workshops''. Lecture Notes in Computer Science, 4743, Springer, 424-434, 2007.

A.A. Shah, D. Barthel, and N. Krasnogorbr
'''Protein Structure Comparison, Analysis and Clustering: An overview of the ProCKSI Decision Support System.'''br
In ''Proceedings of the 4th International Biotechnology Symposium (IBS 2007)''.br
University of Sindh, Pakistan, Nov.4-8, 2007.

D. Barthel, J.D. Hirst, J. Blazewicz, and N. Krasnogorbr
'''ProCKSI: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures'''br
Late-Breaking Results, ''5th European Conference on Computational Biology (ECCB06)'', Israel, 2007.

F. Birzele, J. E. Gewehr, G. Csaba, and R. Zimmer ([http://doi.wiley.com/10.1002/prot.20331 publisher]) br
'''Vorolign - Fast Structural Alignment using Voronoi Contacts'''br
''Bioinformatics'' 23, e205-e211, 2007.

2005
D.A. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J.D. Hirst, and E.K. Burke ([http://www.sciencedirect.com/science/article/B6V05-4DV1959-2/2/aabb4b5cb25dabb343c6d7f7109aa615 publisher])br
'''A fuzzy sets based generalization of contact maps for the overlap of protein structures'''br
''Fuzzy Sets and Systems'' 152(1), 101-123, 2005.

Y. Zhang and J. Skolnick ([http://nar.oxfordjournals.org/cgi/content/abstract/33/7/2302 publisher])br
'''TM-align: A protein structure alignment algorithm based on TM-score'''br
''Nucleic Acids Research'' 33, 2302-2309, 2005.

J. Zhu and Y. Weng ([http://doi.wiley.com/10.1002/prot.20331 publisher])br
'''FAST: A Novel Protein Structure Alignment Algorithm'''br
''Proteins: Structure, Function and Bioinformatics'' 14, 417-423, 2005.

C. Bousono-Calzon, A. Oropesa-Garcia, and N. Krasnogor ([http://www.cs.nott.ac.uk/~nxk/PAPERS/s112-01.pdf personal])br
'''Selecting protein fuzzy contact maps through information and structure measures'''br
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.

D.A. Pelta, J.R. Gonzales, and N. Krasnogor ([http://www.cs.nott.ac.uk/~nxk/PAPERS/s112-04.pdf personal])br
'''Protein Structure Comparison through Fuzzy Contact Maps and the Universal Similarity Metric'''br
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.

R. Hoffmann and A. Valencia ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/suppl_2/ii252?etoc publisher])br
'''Implementing the iHOP concept for navigation of biomedical literature'''br
''Bioinformatics'' 21, ii252-ii258, 2005.

2004
N. Krasnogor and D.A. Pelta ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 publisher])br
'''Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric'''br
''Bioinformatics'' 20(7), 1015-1021, 2004.

A. Caprara, G. Lancia, B. Carr, B. Walenz, and S. Istrail ([http://www.liebertonline.com/doi/abs/10.1089/106652704773416876 puslisher])br
'''1001 optimal PDB structure alignments: Integer Programming methods for finding the maximum contact map overlap'''br
''Journal of Computational Biology'' 11(1), 27-52, 2004.

R. Hoffmann and A. Valencia ([http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html publisher])br
'''A Gene Network for Navigating the Literature'''br
''Nature Genetics'' 36, 664-664, 2004.

N. Krasnogor and D.A. Pelta ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015 publisher])br
'''Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric'''br
''Bioinformatics'' 20(7), 1015-1021, 2004.

2000
L. Holm and J. Park ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/6/566 publisher])br
'''!DaliLite workbench for protein structure comparison'''br
''Bioinformatics'' 16, 566-567, 2000.

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne ([http://nar.oxfordjournals.org/cgi/content/abstract/28/1/235 publisher])br
'''The Protein Data Bank'''br
''Nucleic Acids Res.'' 28, 235–242, 2000.

J. Bingham, S. Sudarsanam ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/7/660 publisher])br
'''Visualizing large hierarchical clusters in hyperbolic space'''br
''Bioinformatics'' 16(7), 660-661, 2000.

1998
I. N. Shindyalov and P. E. Bourne ([http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/7/660 publisher])br
'''Protein structure alignment by incremental combinatorial extension (CE) of the optimal path'''br
''Protein Engineering'' 11, 739-747, 1998. 1997
E.A. Merritt and D.J. Baconbr
'''Raster3D: photorealistic molecular images'''br
''Meth. Enzymol.'' 277, 505-524, 1997. 1996
L. Holm and C. Sander ([http://www.sciencemag.org/cgi/content/abstract/273/5275/595 publisher])br
'''Mapping the protein universe'''br
''Science'' 273, 595-602, 1996. 1993
L. Holm and C. Sander ([http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&dopt=Citation&list_uids=8377180 publisher]))br
'''Protein Structure Comparison by Alignment of Distance Matrices'''br
''J. Mol. Biol.'' 223, 123-138, 1993. 1991
P.J. Kraulisbr
'''MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures'''br
''J. Appl. Cryst.'' 24, 946-950, 1991.