ProCKSI

= Further Literature =

== 2008 ==

D.A. Pelta, J.R. Gonzalez, and M. Moreno Vega[[br]]

'''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. Krasnogor[[br]]

'''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. Krasnogor[[br]]

'''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. Bacon[[br]]

'''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. Kraulis[[br]]

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

''J. Appl. Cryst.'' 24, 946-950, 1991.