DataResources » History » Version 3
Version 2 (Anonymous, 07/11/2007 02:51 PM) → Version 3/4 (Anonymous, 07/11/2007 02:51 PM)
h1. = Data Resources
h1. =
= Dataset
=
Protein structures can be obtained using the following ways:[[br]]
* *User*: '''User''': Upload of arbitratry protein structures[[br]]
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{{{+}}} no maintenance[[br]]
{{{-}}} user needs to upload entire dataset
* *Local repository*: '''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]]
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{{{+}}} "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]] '''Local''': ProCKSI Cluster[[br]]
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{{{+}}} exclusive use of resources [[br]]
{{{+}}} direct access to database[[br]]
{{{+}}} usage: any software[[br]]
{{{-}}} high maintenance[[br]]
{{{-}}} high acquisition costs[[br]]
* *Remote*: '''Remote''': University Cluster or the Grid
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{{{+}}} low maintenance[[br]]
{{{+}}} no acquisition costs[[br]]
{{{+/-}}} usage: software that can be installed & runs in this environment[[br]]
{{{+/-}}} shared use of resources[[br]]
* *External*: '''External''': Web services
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{{{+}}} low maintenance[[br]]
{{{+}}} no acquisition costs[[br]]
{{{+/-}}} shared use of resources[[br]]
{{{-}}} usage: only for provided services[[br]]
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
** '''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: "online":http://zhang.bioinformatics.ku.edu/TM-align/, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/TMalign.tgz
** [http://zhang.bioinformatics.ku.edu/TM-align/ online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/TMalign.tgz repository]
* FAST: "online":http://biowulf.bu.edu/FAST/, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/FAST.tgz?format=raw
** [http://biowulf.bu.edu/FAST/ online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/FAST.tgz?format=raw repository]
* CE: "online":http://cl.sdsc.edu/, "repository":https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/CE.tgz
** [http://cl.sdsc.edu/ online], [https://psiren.cs.nott.ac.uk/projects/procksi/browser/Externals/Comparison/CE.tgz repository]
* LGA: "online":http://www.llnl.gov/ipac/technology/software/softwaretitles/lga.php
** FlexProt: "online":http://bioinfo3d.cs.tau.ac.il/FlexProt/
** [http://www.llnl.gov/ipac/technology/software/softwaretitles/lga.php online]
* !FlexProt: [http://bioinfo3d.cs.tau.ac.il/FlexProt/ online]
* SSM: "online":http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html [http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html online]
Overview of *Web Services*:[[br]]
** '''Web Services''':[[br]]
* CATH-SSAP (in development): "WSDL":http://www.cathdb.info/wsdl/Ssap.wsdl
** [http://www.cathdb.info/wsdl/Ssap.wsdl WSDL]
* Vorolign (in development): "online":http://www.bio.ifi.lmu.de/Vorolign/
** [http://www.bio.ifi.lmu.de/Vorolign/ online]
* Web services at the "Barcelona [http://inb.bsc.es/services/documentation/services.php Barcelona Supercomputing Center":http://inb.bsc.es/services/documentation/services.php
** Center]
* Web services at the "European [http://www.ebi.ac.uk/Tools/webservices/ European Bioinformatics Institute":http://www.ebi.ac.uk/Tools/webservices/
h1. 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/":http://www.pdb.org/]
[http://www.cathdb.info/]
* SCOP: "* [http://scop.mrc-lmb.cam.ac.uk/scop/]
* iHOP: [http://www.ihop-net.org/":http://scop.mrc-lmb.cam.ac.uk/scop/] [http://www.ihop-net.org/]