ProCKSI

= Data Resources =

= Dataset =

Protein structures can be obtained using the following ways:[[br]]

 * '''User''': Upload of arbitratry protein structures[[br]]

   {{{+}}} no maintenance[[br]]

   {{{-}}} user needs to upload entire dataset

 * '''Online repository''': PDB repository ([http://www.pdb.org/])[[br]]

   {{{+}}} repository is maintained externaly[[br]]

   {{{-}}} entire dataset needs to be downloaded on demand

 * '''Local repository''': Copy of the PDB repository[[br]]

   {{{+}}} "caching" of structures: quick access[[br]]

   {{{+}}} low data volume to be transfer[[br]]

   {{{-}}} synchronisation with official repository neccessary (nightly/weekly updates)[[br]]

   {{{-}}} "caching" of structures: download from online repository if not available localy

= Similarity Comparisons =

Similarity comparisons can be performed using the following resources:[[br]]

 * '''Local''': ProCKSI Cluster[[br]]

   {{{+}}} exclusive use of resources [[br]]

   {{{+}}} direct access to database[[br]]

   {{{+}}} usage: any software[[br]]

   {{{-}}} high maintenance[[br]]

   {{{-}}} high acquisition costs[[br]]

 * '''Remote''': University Cluster or the Grid

   {{{+}}} low maintenance[[br]]

   {{{+}}} no acquisition costs[[br]]

   {{{+/-}}} usage: software that can be installed & runs in this environment[[br]]

   {{{+/-}}} shared use of resources[[br]]

 * '''External''': Web services

   {{{+}}} low maintenance[[br]]

   {{{+}}} no acquisition costs[[br]]

   {{{+/-}}} shared use of resources[[br]]

   {{{-}}} usage: only for provided services[[br]]

Overview of '''Local Methods''':

  * !DaliLite: [http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/DaliLite.tgz repository]

  * TM-align: [http://zhang.bioinformatics.ku.edu/TM-align/ online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/TMalign.tgz repository]

  * FAST: [http://biowulf.bu.edu/FAST/ online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/FAST.tgz?format=raw repository]

  * CE: [http://cl.sdsc.edu/ online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/CE.tgz repository]

  * LGA: [http://www.llnl.gov/ipac/technology/software/softwaretitles/lga.php online]

  * !FlexProt: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ online]

  * SSM: [http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html online]

Overview of '''Web Services''':[[br]]

  * CATH-SSAP (in development): [http://www.cathdb.info/wsdl/Ssap.wsdl WSDL]

  * Vorolign (in development): [http://www.bio.ifi.lmu.de/Vorolign/ online]

  * Web services at the [http://inb.bsc.es/services/documentation/services.php Barcelona Supercomputing Center]

  * Web services at the [http://www.ebi.ac.uk/Tools/webservices/ European Bioinformatics Institute]

= Further Information =

Further information for one given protein structure can be obtained from the following sources:

 * PDB repository: [http://www.pdb.org/]

 * CATH: [http://www.cathdb.info/]

 * SCOP: [http://scop.mrc-lmb.cam.ac.uk/scop/]

 * iHOP: [http://www.ihop-net.org/]