Overview of application CoPS Comparison of Protein Structures

1
Overview of application CoPS (Comparison of
Protein Structures)

• D.Ludviga
• IMCS UL (SigmaNet)

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Outline

• About CoPS (scientific value)
• What's new?
• Challenges (mentioned during 1AHM)
• Our solution
• Collaboration possibilities.

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About CoPS (scientific value)

• Started at the beginning of BG-II as the pilot
  application
• developed by Dr. Natalja Kurbatova and Asoc.
  Prof. Juris Viksna
• Field Bioinformatics
• It has taken biologists some 230 years to
  identify and describe three quarters of a million
  insects if there are indeed at least thirty
  million ... then, working as they have in the
  past, insect taxonomists have ten thousand years
  of employment ahead of them.
• R.Leakey and L.Roger

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About CoPS

• Assumption - protein structures have evolved by
  a stepwise process, each step involving a small
  change in the structure.
• Comparison of protein structures using
  Evolutionary Secondary Structures Matching (ESSM)
  algorithm
• ESSM was created for pair wise comparison of
  structures that allow to identify fold mutations
  and to estimate evolutionary relationship between
  proteins.
• For exploration of evolution of protein
  structures all-against-all comparison have to be
  done
• Application needs
• Protein data base (data set description files are
  stored)
• PDB (3D), FASTA (.txt), structural elements
• size 8 GB (2.3GB if compressed)
• Total number of tasks - 20 451 945, divided in
  410 files

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About CoPS

• Application consists of
• jdl.essm - JDL file for submitting ESSM (CoPS)
  job
• essm.sh - shell script that is executed on WN
  once the job starts
• database.tar.gz - archive of the protein database
  with protein descriptions, which is extracted on
  the WN before anything else starts
• essm.linux - statically compiled executable for
  ESSM(CoPS) that works on Scientific Linux CERN
  4, 32-bit binary
• pairs.txt - sample calculation file that contains
  pair comparisons
• At the end of each job result file pairs.result
  is generated
• Afterwards visualized using a self made tool.
• developed using one of GRADE components

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About CoPS
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Whats new?

• Developed (results received)
• 2 weeks.
• Implemented in Migrating Desktop
• Presented/demonstrated on OGF25/EGEE Users Forum
  in Catania, Italy
• Demo

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Challenges and our solution

• Challenges
• Transport the data
• 410 x 2.3GB 950GB
• VOMS-proxy.
• Solutions
• The needed data was installed on separate
  clusters software directories (developed
  devoted protein clusters)
• Myproxy

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Results

• The results of the ESSM algorithm were
  successfully used for the exploration of the CATH
  fold space by using fold space graphs for
  representation of comparison results and
  estimation of "evolution distance" on the basis
  of observed changes.
• The results obtained in the application can be
  represented as a few steps toward the creation of
  an general protein evolution model.

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Collaboration

• Computer science is no more about computers than
  astronomy is about telescopes
• E.W.Dijkstra
• Continue collaboration with biologists in LU
• Develop an VO or just devoted servers
• PDB can be installed on a clusters VO software
  directory
• To speed up execution of jobs and avoid per-job
  download and extraction of these databases.

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Thank you!