Further Literature¶
2008¶
D.A. Pelta, J.R. Gonzalez, and M. Moreno Vega (publisher)
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)
Web & Grid Technologies in Bioinformatics, Computational Biology and Systems Biology: A Review.
Current Bioinformatics, 3, 10-31, 2008.
2007¶
D. Barthel, J.D. Hirst, J. Błażewicz, E.K. Burke, and N. Krasnogor (publisher)
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, bibtex)
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)
Vorolign - Fast Structural Alignment using Voronoi Contacts
Bioinformatics 23, e205-e211, 2007.
2005¶
D.A. Pelta, N. Krasnogor, C. Bousono-Calzon, J.L. Verdegay, J.D. Hirst, and E.K. Burke (publisher)
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)
TM-align: A protein structure alignment algorithm based on TM-score
Nucleic Acids Research 33, 2302-2309, 2005.
J. Zhu and Y. Weng (publisher)
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)
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)
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)
Implementing the iHOP concept for navigation of biomedical literature
Bioinformatics 21, ii252-ii258, 2005.
2004¶
N. Krasnogor and D.A. Pelta (publisher)
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)
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)
A Gene Network for Navigating the Literature
Nature Genetics 36, 664-664, 2004.
N. Krasnogor and D.A. Pelta (publisher)
Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric
Bioinformatics 20(7), 1015-1021, 2004.
2000¶
L. Holm and J. Park (publisher)
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)
The Protein Data Bank
Nucleic Acids Res. 28, 235–242, 2000.
J. Bingham, S. Sudarsanam (publisher)
Visualizing large hierarchical clusters in hyperbolic space
Bioinformatics 16(7), 660-661, 2000.
1998¶
I. N. Shindyalov and P. E. Bourne (publisher)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
Protein Engineering 11, 739-747, 1998.
1997¶
E.A. Merritt and D.J. Bacon
Raster3D: photorealistic molecular images
Meth. Enzymol. 277, 505-524, 1997.
1996¶
L. Holm and C. Sander (publisher)
Mapping the protein universe
Science 273, 595-602, 1996.
1993¶
L. Holm and C. Sander (publisher)
Protein Structure Comparison by Alignment of Distance Matrices
J. Mol. Biol. 223, 123-138, 1993.
1991¶
P.J. Kraulis
MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures
J. Appl. Cryst. 24, 946-950, 1991.