Compiling eFindSite under Mac OS X

eFindSite is a ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins and is described in detail in a recent publication. 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):551-567 DOI It employs a collection of effective algorithms, including highly sensitive meta-threading approaches, improved clustering techniques, advanced machine learning methods and reliable confidence estimation systems.

A reader sent in detailed instructions for installation

• OS X has perl already installed (with XCode/Command Line Tools I think)

• Install perl cpanm module:

  sudo cpan App::cpanminus

• type yes for automatic configuration

• Install other perl modules:

  sudo cpan File::Temp sudo cpan File::Slurp

• zlib should already be installed

• Download gzstream: http://www.cs.unc.edu/Research/compgeom/gzstream/gzstream.tgz

• Build gzstream:

  cd ~/Downloads/gzstream/ make

• I couldn't manage to download f2c from the link provided - ftp.netlib.org seems to be down? (Should be www.netlib.org/f2c )

• Found a mirror: http://netlib.sandia.gov/cgi-bin/netlib/netlibfiles.tar?filename=netlib/f2c

• Download, untar, then also unzip libf2c.zip inside the f2c directory.

  cd ~/Downloads/f2c/libf2c/ make f2c.h -f makefile.u make -f makefile.u

• Download libsvm: http://www.csie.ntu.edu.tw/~cjlin/cgi-bin/libsvm.cgi?+http://www.csie.ntu.edu.tw/~cjlin/libsvm+tar.gz

• Build libsvm:

  cd ~/Downloads/libsvm-3.17/ make ar cr libsvm.a svm.o

• Download eFindSite: http://brylinski.cct.lsu.edu/content/efindsite-standalone-package

• Untar it. We then need to copy the dependencies into the lib directory:

  cp ~/Downloads/gzstream/gzstream.h ~/Downloads/efindsite-1.1/lib/gzstream.h cp ~/Downloads/gzstream/libgzstream.a ~/Downloads/efindsite-1.1/lib/libgzstream.a cp ~/Downloads/f2c/libf2c/f2c.h ~/Downloads/efindsite-1.1/lib/f2c.h cp ~/Downloads/f2c/libf2c/libf2c.a ~/Downloads/efindsite-1.1/lib/libf2c.a cp ~/Downloads/libsvm-3.17/svm.h ~/Downloads/efindsite-1.1/lib/svm.h cp ~/Downloads/libsvm-3.17/libsvm.a ~/Downloads/efindsite-1.1/lib/libsvm.a

• gcc 4.4 is required to properly compile eFindSite (Xcode has 4.2.1 I think)

• install MacPorts: http://www.macports.org/

• update software repos:

  sudo port selfupdate sudo port install gcc44

• in eFindSite Makefile (~/Downloads/efindsite-1.1/src/Makefile) change "CXX = g++" to "CXX = g++-mp-4.4"

• Then build it:

  cd ~/Downloads/efindsite-1.1/src/ make