ProCKSI

h1. Further Literature

h2. 2008

D.A. Pelta, J.R. Gonzalez, and M. Moreno Vega ("publisher":http://dx.doi.org/10.1186%2F1471-2105-9-161)

*A simple and fast heuristic for protein structure comparison*

_BMC Bioinformatics_, 2008 (to appear)

A.A. Shah, D. Barthel, P. Łukasiak, J. Błażewicz, and N. Krasnogor ("publisher":http://dx.doi.org/10.2174/157489308783329850)

*Web & Grid Technologies in Bioinformatics, Computational Biology and Systems Biology: A Review.*

_Current Bioinformatics_, 3, 10-31, 2008.

h2. 2007

D. Barthel, J.D. Hirst, J. Błażewicz, E.K. Burke, and N. Krasnogor ("publisher":http://www.biomedcentral.com/1471-2105/8/416/abstract)

*The ProCKSI Server: A Decision Support System for Protein (Structure) Comparison, Knowledge, Similarity and Information.* 

_BMC Bioinformatics_ 2007, 8, 416.

A.A. Shah, D. Barthel, and N. Krasnogor ("publisher":http://www.springerlink.com/content/90n46423p200502r/, "bibtex":http://dblp.uni-trier.de/rec/bibtex/conf/ispa/ShahBK07)

*Grid and Distributed Public Computing Schemes for Structural Proteomics: A Short Overview.*

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

*Protein Structure Comparison, Analysis and Clustering: An overview of the ProCKSI Decision Support System.*

In _Proceedings of the 4th International Biotechnology Symposium (IBS 2007)_.

University of Sindh, Pakistan, Nov.4-8, 2007. 

D. Barthel, J.D. Hirst, J. Blazewicz, and N. Krasnogor

*ProCKSI: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures*

Late-Breaking Results, _5th European Conference on Computational Biology (ECCB06)_, Israel, 2007.

F. Birzele, J. E. Gewehr, G. Csaba, and R. Zimmer ("publisher":http://doi.wiley.com/10.1002/prot.20331) 

*Vorolign - Fast Structural Alignment using Voronoi Contacts*

_Bioinformatics_ 23, e205-e211, 2007.

h2. 2005

D.A. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J.D. Hirst, and E.K. Burke ("publisher":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*

_Fuzzy Sets and Systems_ 152(1), 101-123, 2005.

Y. Zhang and J. Skolnick ("publisher":http://nar.oxfordjournals.org/cgi/content/abstract/33/7/2302)

*TM-align: A protein structure alignment algorithm based on TM-score*

_Nucleic Acids Research_ 33, 2302-2309, 2005.

J. Zhu and Y. Weng ("publisher":http://doi.wiley.com/10.1002/prot.20331)

*FAST: A Novel Protein Structure Alignment Algorithm*

_Proteins: Structure, Function and Bioinformatics_ 14, 417-423, 2005.

C. Bousono-Calzon, A. Oropesa-Garcia, and N. Krasnogor ("personal":http://www.cs.nott.ac.uk/~nxk/PAPERS/s112-01.pdf)

*Selecting protein fuzzy contact maps through information and structure measures*

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 ("personal":http://www.cs.nott.ac.uk/~nxk/PAPERS/s112-04.pdf)

*Protein Structure Comparison through Fuzzy Contact Maps and the Universal Similarity Metric*

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 ("publisher":http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/suppl_2/ii252?etoc)

*Implementing the iHOP concept for navigation of biomedical literature*

_Bioinformatics_ 21, ii252-ii258, 2005.

h2. 2004

N. Krasnogor and D.A. Pelta ("publisher":http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015)

*Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric*

_Bioinformatics_ 20(7), 1015-1021, 2004.

A. Caprara, G. Lancia, B. Carr, B. Walenz, and S. Istrail ("puslisher":http://www.liebertonline.com/doi/abs/10.1089/106652704773416876)

*1001 optimal PDB structure alignments: Integer Programming methods for finding the maximum contact map overlap*

_Journal of Computational Biology_ 11(1), 27-52, 2004.

R. Hoffmann and A. Valencia ("publisher":http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html)

*A Gene Network for Navigating the Literature*

_Nature Genetics_ 36, 664-664, 2004.

N. Krasnogor and D.A. Pelta ("publisher":http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/7/1015)

*Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric*

_Bioinformatics_ 20(7), 1015-1021, 2004.

h2. 2000

L. Holm and J. Park ("publisher":http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/6/566)

*DaliLite workbench for protein structure comparison*

_Bioinformatics_ 16, 566-567, 2000.

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne ("publisher":http://nar.oxfordjournals.org/cgi/content/abstract/28/1/235)

*The Protein Data Bank*

_Nucleic Acids Res._ 28, 235–242, 2000.

J. Bingham, S. Sudarsanam ("publisher":http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/7/660)

*Visualizing large hierarchical clusters in hyperbolic space*

_Bioinformatics_ 16(7), 660-661, 2000.

h2. 1998

I. N. Shindyalov and P. E. Bourne ("publisher":http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/7/660)

*Protein structure alignment by incremental combinatorial extension (CE) of the optimal path*

_Protein Engineering_ 11, 739-747, 1998.

h2. 1997

E.A. Merritt and D.J. Bacon

*Raster3D: photorealistic molecular images*

_Meth. Enzymol._ 277, 505-524, 1997.

h2. 1996

L. Holm and C. Sander ("publisher":http://www.sciencemag.org/cgi/content/abstract/273/5275/595)

*Mapping the protein universe*

_Science_ 273, 595-602, 1996.

h2. 1993

L. Holm and C. Sander ("publisher":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*

_J. Mol. Biol._ 223, 123-138, 1993.

h2. 1991

P.J. Kraulis

*MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures*

_J. Appl. Cryst._ 24, 946-950, 1991.