Data Resources¶

Dataset¶

Protein structures can be obtained using the following ways:br

• User: Upload of arbitratry protein structuresbr
  

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  * *Local repository*: Copy of the PDB repository[[br]]
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  h1. Similarity Comparisons
  
  Similarity comparisons can be performed using the following resources:[[br]]
  * *Local*: [[ProCKSI]] Cluster[[br]]
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  * *Remote*: University Cluster or the Grid
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  * *External*: Web services
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  Overview of *Local Methods*:
  ** DaliLite: "online":http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/DaliLite.tgz
  ** TM-align: "online":http://zhang.bioinformatics.ku.edu/TM-align/, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/TMalign.tgz
  ** FAST: "online":http://biowulf.bu.edu/FAST/, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/FAST.tgz?format=raw
  ** CE: "online":http://cl.sdsc.edu/, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/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*:[[br]]
  ** 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: "* CATH: [http://www.cathdb.info/":http://www.pdb.org/]
  * SCOP: "* iHOP: [http://www.ihop-net.org/":http://scop.mrc-lmb.cam.ac.uk/scop/]