Data Resources¶

Dataset¶

Protein structures can be obtained using the following ways:

• User: Upload of arbitratry protein structures
• Local repository: Copy of the PDB repository

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, source:Externals/Comparison/DaliLite.tgz
• TM-align: online, source:Externals/Comparison/TMalign.tgz
• FAST: online, source:Externals/Comparison/FAST.tgz
• CE: online, source:Externals/Comparison/CE.tgz
• LGA: online
• FlexProt: online
• SSM: online

Overview of Web Services:

• CATH-SSAP (in development): WSDL
• Vorolign (in development): online
• Web services at the Barcelona Supercomputing Center
• Web services at the 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/