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''': Web Services Overview:[[br]]
* !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] [http://www.cathdb.info/wsdl/Ssap.wsdl]
* Vorolign (in development): [http://www.bio.ifi.lmu.de/Vorolign/ online] development)
* 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/]