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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:

  1. 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.

  2. 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:

  1. First you have to download eFindSite from here https://github.com/michal-brylinski/efindsite and unzip:

    • [local]$ unzip efindsite-master.zip
    • [local]$ cd efindsite-master/
    • [efindsite-master]$ make
    • [efindsite-master]$ ls bin/
    • [bin]$ ./efindsite
  2. 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/
  3. 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
  4. 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

  • 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)
  • Open the output files and check to make sure the files contain data.

  • If the output files are empty, go back and check the script.

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Ligand binding site prediction and virtual screening

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