eFindSite
eFindSite is a tool that predicts binding pockets, residues and ligands from a given protein structure by threading methods.
This README file is written by Snigdha Thumma.
If you find this tool useful, please cite these following papers:
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Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.
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Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.
Prerequisites:
- GCC compiler version 4.8.5+
- Perl version 5.16.3+
Example:
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First you have to download eFindSite from here
https://github.com/michal-brylinski/efindsiteand unzip:[local]$ unzip efindsite-master.zip[local]$ cd efindsite-master/[efindsite-master]$ make[efindsite-master]$ ls bin/[bin]$ ./efindsite
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Then install the eFindSite template libraries from here
https://osf.io/mp343/( download the latest available library ) and unpack the tarball:[local]$ mkdir libraries[local]$ tar xzf efindsite-lib-2018-04.tar.gz -C /usr/local/libraries/[local]$ tar xzf efindsite-mod-2016-06.tar.gz -C /usr/local/libraries/
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Before running eFindSite, you need to set several environmental variables.
- eFindSite
[home]$ export EF_LIB=/usr/local/libraries/efindsite-lib-2018-04[home]$ export EF_MOD=/usr/local/libraries/efindsite-mod-2016-06
- eFindSite
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After the environmental variables are set, it’s time to run the eFindSite and efindsite_screen
[library]$ /usr/local/efindsite-master/bin/efindsite -s 13gsA.pdb -t 13gsA-efindsite.lst -e 13gsA.profile -o 13gsA-efindsite_test[library]$ /usr/local/efindsite-master/bin/efindsite_screen -p 13gsA-efindsite.pockets.dat -s escreen-keggcomp-mar2012.gz -o 13gsA-escreen-keggcomptest[library]$ /usr/local/efindsite-master/bin/efindsite_screen -p 13gsA-efindsite.pockets.dat -s escreen-zinc12_nr-mar2012.gz -o 13gsA-escreen-zinc12_nrtest
Mandatory arguments for eFindSite
| Parameter | Optional | Name | Description |
|---|---|---|---|
| -s | N | input_file | Is the target protein structure in PDB format; you can use either experimental structure or protein model |
| -t | N | template-fun | Is a text file that contains information on protein templated identified for your target e.g. by eThread |
| -e | N | seq.profile | Is a sequence profile of the target; it can be generated by PROFILPRO |
| -o | N | output_name | Is used to save five output files with different extensions that store dinging site prediction results |
Mandatory arguments for efindsite_scr
| Parameter | Optional | Name | Description |
|---|---|---|---|
| -p | N | pocket.dat | pocket.dat is a file containing the predicted binding pockets by eFindSite |
| -s | N | cmp_lib | cmp_lib is a compound library used for virtual screening |
| -o | N | output_file | output_file will contain ranked library compounds assigned with a Tanimoto score and Z-score |
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If eFindSite runs successfully, it should yield 5 output files with user defined input name. ** For example: the user defined input file, 13gsA-efindsite_test, has 5 outputs as seen below*
- 13gsA-efindsite_test.pockets.dat (detailed info on predicted pockets)
- 13gsA-efindsite_test.pockets.pdb (predicted pockets in PDB format)
- 13gsA-efindsite_test.alignments.dat (structure alignments of templates into the target in FASTA format)
- 13gsA-efindsite_test.templates.pdb (template structures aligned onto the target in PDB format)
- 13gsA-efindsite_test.ligands.sdf (extracted binding ligands in SDF format)
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Open the output files and check to make sure the files contain data.
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If the output files are empty, go back and check the script.