Speakers
Description
Conclusions and Future Work
The development and implementation of this application will provide significant benefits and a clear starting point for other biologists, who are working with similar protein applications. The CoPS application is conspicuous for the large data amount (Protein database ~ 8GB), which is being used in every parallel job.The specific requirements of the CoPS application are a good motivation to create a separate VO, which would be later used by other biologists as well.
Justification for delivering demo and technical requirements (ONLY for demonstrations)
We intend to show a live-demo of the CoPS life cycle, starting from defining the input parameters, submitting the job to the BalticGrid-II testbed, job monitoring, and ending with visualization of the results. The application is run within the “Migrating Desktop” – advanced GUI that hides the complexity of the grid and makes access to the resources easy and transparent. We believe that the interesting scientific content combined with intuitive interface will attract the audience’s attention.
URL for further information
http://www.balticgrid.org
Detailed analysis
The CoPS application offers a method applied for exploration of potential evolutionary relationships between the CATCH protein domains and their characteristics and uses the so-called 3D graphs approach. This is a convenient tool which allows easy detection of not only structural similarity but also of possible fold mutations between these proteins.
This method consists of two stages:
1) All-against-all comparison of CATCH domains by the ESSM software;
2) Construction of fold space graphs on the basis of the output of the 1st stage. This approach, useful in the exploration of basic tendencies in evolution of the protein structures and functions, is based on the assumption that protein structures, similarly to sequences, have evolved by a stepwise process, each step involving a small change in protein fold.
The application gridified within BalticGrid-II is using the Protein DataBase (PDB) and comparing several proteins independently or in parallel.
Impact
The CoPS application uses BalticGrid-II computing infrastructure to compare protein structures. It can automatically identify different types of protein structure mutations between a pair of proteins. It should be noted, that for exploration of protein structures all-against-all comparison has to be done. The Grid infrastructure is providing a possibility to process the whole protein database, for example the CATH database, where the number of pairwise comparisons isa few billions.
Due to the need of powerful computing resources and large network bandwidth, the CoPS is a good example of anapplication which benefits from the usage of the BalticGrid-II infrastructure.
Keywords
protein structures, grid computing, ESSM, Migrating Desktop, BalticGrid-II
