ProCKSI

h1. Data Resources

h1. Dataset

Protein structures can be obtained using the following ways:

* *User*: Upload of arbitratry protein structures

* *Local repository*: Copy of the PDB repository

h1. Similarity Comparisons

Similarity comparisons can be performed using the following resources:

* *Local*: ProCKSI Cluster

* *Remote*: University Cluster or the Grid

* *External*: Web services

Overview of *Local Methods*:

** DaliLite: "online":http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads, source:Externals/Comparison/DaliLite.tgz

** TM-align: "online":http://zhang.bioinformatics.ku.edu/TM-align/, source:Externals/Comparison/TMalign.tgz

** FAST: "online":http://biowulf.bu.edu/FAST/, source:Externals/Comparison/FAST.tgz

** CE: "online":http://cl.sdsc.edu/, source:Externals/Comparison/CE.tgz

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

** FlexProt: "online":http://bioinfo3d.cs.tau.ac.il/FlexProt/

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

Overview of *Web Services*:

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

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

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

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

h1. 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/