The CaspDB database can be accessed at http://caspdb.sanfordburnham.org for the online acsess of caspase cleavage sites prediction of reviewed human proteins. All caspase cleavage sites were predicted using Random Forest (RF) machine-learning algorithm and stored in CaspDB. Caspase cleavage sites prediction uses position weight matrix, secondary structure, disorder region information. Each substrate has been linked to their orthologous and also integrated to SNPs and PTMs information. The method used for predicting caspase cleavage sites have been determined by statistical analysis of experimentally verified cleavage sites from MerCASBA database. This method was tested using the 10-fold cross-validation approach and acheives high accuracy (98%).

Query type

There are two types of query for retreiving cleavage sites of substrates. Firstly, using Uniprot ID or Uniprot name users can access cleavage sites at Asp postion or both Asp and Glu position at P1 position. CaspDB can also retreive substrates using motif search.

Motif search can be used in several ways:

1. Using simple strings. example: DEVD
It will list all the substrates which has DEVD.

2. If you know putative or experimentally cleavage site then you must marked as '-' in motif. example: DEVD-A

3. If you want to search motif which has any residue in between residues use '.'
example: DE.D-A or DE.D

4. If you want to search motif where at a given position either of one residue can present, use '[]'
example: DEVD-[AGST] It will search Ala or Gly or Ser or Thr at P1' position along with DEVD motif.

5. For multiple motif search use '|'
example: DEVD|GEVD|EEVD

Results of Uniprot search

Caspase cleavage prediction results for RIPK1 is shown in tabular form.



Using Compare button human orthologous cleavage and pair-wise alignnment can be retreived:




Multiple sequence alignments of all orthologous proteins can be retreived using Start Jalview:



Results of motif search


Datasets

The predicted cleavage sites of human proteins and orthologous proteins can be downloaded by clicking following link.

HumanDownload file
MouseDownload file
Branchiostoma floridaeDownload file
Capsaspora owczarzaki (strain ATCC 30864)Download file
Branchiostoma floridaeDownload file
Caenorhabditis elegansDownload file
Danio rerioDownload file
Drosophilla melanogasterDownload file
Nematostella vectensisDownload file
Schistosoma mansoniDownload file
Strongylocentrotus purpuratusDownload file
Trichoplax adhaerensDownload file
Xenopus tropicalisDownload file

How to enable Java-Plugins on websites

Please consider following steps described in Java provided help on how to enable Java-Plugins on websites.

For WinXP/Win 7, go to System Settings => Java => Security => add caspdb.sanfordburnham.org to the allowed servers list.

For Mac, open Chrome settings => Settings => Advanced Settings => Privacy => Content Settings => Plug-Ins => Manage Exceptions => add caspdb.sanfordburnham.org to allowed servers.

CaspDB uses Java applet- an uncertified applet and structure viewing is hence blocked by default. In order to solve this, please go to Control Panel-> Java-> Security-> Edit site list and add the CaspDB URL caspdb.sanfordburnham.org to the exception list. For more information go to http://www.java.com/en/download/exception_sitelist.jsp

Java Applet does not work in Safari and Chrome in Mac OS

Apple supplies its own Java. Java 7 from Oracle is not compatible with Chrome and Safari in Mac. To restore Apple's Java SE 6, please refer Apple support for details.

These 2 commands will restore Java SE 6, for running Java Applet.

sudo mv /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/ /Library/Internet\ Plug-Ins/Disabled\ Plug-Ins/

sudo ln -sf /System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPlugin2_NPAPI.plugin/ /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin

For Safari

sudo ln -sf /System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPlugin2_NPAPI.plugin /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin