Template libraries

eFindSite template library

Download eFindSite template library from here, unpack the tarball:

[local]$ mkdir libraries

[local]$ tar xzf efindsite-lib-jan2012.tar.gz -C libraries/

Optionally, you can create a symlink to the latest eFindSite library. This is useful to quickly switch between different library versions.

[local]$ cd libraries

[libraries]$ ln -s efindsite-lib-jan2012 efindsite-lib-latest

Threading library and mapping files

eFindSite needs a mapping file to map threading templates to its own ligand-bound templates. If you use eThread as a threading algorithm, you can skip this step as the mapping files are already included in the eFindSite library (e.g. ethread-lib-jan2012.map) and are available from the download page. However, you can make eFindSite work with any threading method and/or template library by using maping files:

[efindsite-lib-latest]$ ../../efindsite-1.0/bin/efindsite_map -t mythreadlib.fasta -p pdb.fasta -o mythread-efindsite.map

You can find pdb.fasta in efindsite-lib-latest/. The file mythreadlib.fasta should contain a complete (all templates) library that you are using in threading. It should be FASTA formatted, exactly as pdb.fasta. Note that for a given threading algorithm and the corresponding library, the mapping file (e.g. mythread-efindsite.map) needs to be created only once.

In order to use efindsite_map, you need to have NCBI BLAST installed on your system. Furthermore, formatdb and blastall programs should be available from a default search path; you can check this using which:

[home]$ which formatdb blastall

/usr/local/bin/formatdb
/usr/local/bin/blastall

Of course, /usr/local/bin/ can be different on your system.

 

© Michal Brylinski
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