ProCKSI

h1. Papers

h2. 2008

A.A. Shah, G. Folino, D. Barthel, and N. Krasnogor ("publisher":http://dx.doi.org/10.1109/ISPA.2008.41)

*Performance Evaluation of Protein Structure Comparison Algorithms Under Integrated Resource Management Environment for MPI Jobs*

In _Proceedings of International Symposium on Parallel and Distributed Applications (ISPA2008)_.

Sydney, Dec 10-12, 2008. 

G. Folino, A.A. Shah, D. Barthel, and N. Krasnogor ("publisher":http://www.allhands.org.uk/2008/programme/index.cfm)

*Towards a Distributed Framework for Protein (Strucutre) Comparison, Knowledge, Similarity and Information (ProCKSI).*

In _Proceedings of UK eScience All Hands Meeting 2008 (AHM 2008)_.

Edinburgh, Sep.8-11, 2008. 

M.T. Oakley, D. Barthel, Y. Bykov, J.M. Garibaldi, E.K. Burke, N. Krasnogor, and J.D. Hirst ("publisher":http://www.ingentaconnect.com/content/ben/cpps/2008/00000009/00000003/art00006)

*Search Strategies in Structural Bioinformatics.*

_Current Protein and Peptide Science_, 2008, 9(3), 260-274.

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. 

h3. 2006

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

*ProCKSI: A Metaserver for Protein Comparison using Kolmogorov and other Similarity Measures.*

In _Late Breaking Papers. European Conference on Computational Biology_, 2006.

Eilat, Israel, 2006. Peer reviewed CDROM publication.

h3. 2005

D.A. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J. Hirst, and E.K. Burke ("publisher":http://dx.doi.org/10.1016/j.fss.2004.10.017)

*A fuzzy sets based generalization of contact maps for the overlap of protein structures.*

_Journal of Fuzzy Sets and Systems_, 152, 103-123, 2005.

D.A. Pelta, J.R. Gonzales, and N. Krasnogor

*Protein structure comparison through fuzzy contact maps and the universal similarity metric.* 

In _Fourth Conference of the European Society for Fuzzy Logic and Technology and 11 Recontres Francophones sur la Logique Floue et ses Applications (EUSFLAT-LFA'05)_, 1124-1129, Barcelona, Spain, 2005.

h3. 2004

N. Krasnogor ("publisher":http://dx.doi.org/10.1023/B:GENP.0000023687.41210.d7)

*Self-generating metaheuristics in bioinformatics: the protein structure comparison case.*

_Genetic Programming and Evolvable Machines_, 5, 181-201, 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, 1015-1021, 2004.