Title: Automated, Grid-Aware, Three-Tier Protocol for Protein Structure Comparison

Objectives:
Researchers interested in analysing and understanding proteins' sequences, structures and functions have more than 30 genomes at their fingertips (eg. visit NCBI). The comparison of protein structures, and their clustering (according to similarity) is a fundamental aspect of today's biomedical research. The comparison of the 3D structures of protein molecules is a challenging problem. The search for effective solution techniques for this problem is justified because such tools can aid scientists in the development of procedures for drug design, in the identification of new types of protein architecture, in the organization of the known universe of protein structures. They also can help to discover unexpected evolutionary and functional inter-relations between proteins and it could impact upon structure prediction and the methodologies for the evaluation of those predictions.
In this project we are undertaking the implementation of an extended (three-tier) protocol for protein structure comparison building on our recent research progress. The new software will be grid-aware, publicly accessible and will have both an "intuitive" visual interface and also a powerful programmatic application interface (API). It will extend the two-tier protocol described by integrating the Lagrangian Relaxation method for Maximum Contact Map Overlaps and metaheuristics methods for that model. The third layer of the proposed protocol will "harvest" publicly available protein comparison services and will integrate the results of the initial two layers with those harvested from existing software and databases.




Publications

• ProCKSi: A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures
  D. Barthel, J. D. Hirst, J. Blazewicz and N. Krasnogor, Late-Breaking Results, 5th European Conference on Computational Biology (ECCB06), Israel, 2007.
  
• Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric.
  N. Krasnogor and D. A. Pelta, Bioinformatics Vol 20(7), 1015-1021, 2004.
• Self-Generating Metaheuristics in Bioinformatics: The Protein Structure Comparison Case.
  N. Krasnogor, Genetic Programming and Evolvable Machines Vol 5(2), 181-201, 2004.
  
• A Fuzzy Sets Based Generalization of Contact Maps for the Overlap of Protein Structures.
  D. A. Pelta, N. Krasnogor, C. Bousono-Calzon, J. L. Verdegay, J. D. Hirst and E. K. Burke, Journal of Fuzzy Sets and Systems Vol 152(1) 103-123, 200
  
• Selecting protein fuzzy contact maps through information and structure measures.
  C. Bousono-Calzon, A. Oropesa-Garcia and N. Krasnogor, 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.
  
• Protein Structure Comparison through Fuzzy Contact Maps and the Universal Similarity Metric.
  D. A Pelta, J. R. Gonzales and N. Krasnogor, 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 1124-1129.
  

Posters

• Similarity Comparison of Proteins (ATTENTION: server name changed and URL outdated)
  D. Barthel, J. D. Hirst and N. Krasnogor
  BBSRC Bioinformatics and e-Science Grantholders Workshop, Manchester, UK, 2005.
• Similarity Comparison of Proteins (NOTICE: new server name and new URL)
  D. Barthel, J. D. Hirst and N. Krasnogor
  UK e-science All Hands Meeting, Nottingham, UK, 2006.
• The ProCKSi-Server: A meta-server for similarity comparisons of protein structures
  D. Barthel, J. D. Hirst and N. Krasnogor
  5th European Conference on Computational Biology (ECCB06), Israel, 2006. (accepted, postponed to January 2007)

Talks

• Comparisons of Protein Structures: Models, Measures, Metrics and Methods
  
• The ProCKSi-Server:
  A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures (V2)
  5th East Midlands Proteomics Workshop
  Nottingham, United Kingdom, November 2006
• The ProCKSi-Server:
  A Meta-Server for Protein Comparison using Kolmogorov and other Similarity Measures (V3)
  Spanish National Cancer Research Centre (CNIO)
  Madrid, Spain, December 2006

Protocols

• Universal Similarity Metric Protocol for protein structure comparison

• Generalised Fuzzy Sets based Contact Map Overalp Protocol for protein structure comparison

Demonstrations

• D. Barthel and N. Krasnogor, BBSRC Bioinformatics and e-Science Grantholders Workshop, Manchester, UK, 2005.
• D. Barthel, UK e-science All Hands Meeting, Nottingham, UK, 2006.