ProCKSI

= Data Resources =

= Dataset =
Protein structures can be obtained using the following ways:br * '''User''': Upload of arbitratry protein structuresbr {{{+}}} no maintenancebr {{{-}}} user needs to upload entire dataset * '''Online repository''': PDB repository ([http://www.pdb.org/])br</a> {{{+}}} repository is maintained externalybr {{{-}}} entire dataset needs to be downloaded on demand * '''Local repository''': Copy of the PDB repositorybr {{{+}}} "caching" of structures: quick accessbr {{{+}}} low data volume to be transferbr {{{-}}} 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 Clusterbr {{{+}}} exclusive use of resources br {{{+}}} direct access to databasebr {{{+}}} usage: any softwarebr {{{-}}} high maintenancebr {{{-}}} high acquisition costsbr * '''Remote''': University Cluster or the Grid {{{+}}} low maintenancebr {{{+}}} no acquisition costsbr {{{+/-}}} usage: software that can be installed & runs in this environmentbr {{{+/-}}} shared use of resourcesbr * '''External''': Web services {{{+}}} low maintenancebr {{{+}}} no acquisition costsbr {{{+/-}}} shared use of resourcesbr {{{-}}} usage: only for provided servicesbr

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/]