Silicos shape-it as a free alternative to OpenEye ROCS?
Silicos provides shape-it - a C++ program for doing shape matching using gaussian volume.
To compile under Ubunt 12.04
sudo apt-get install libopenbabel-dev libopenbabel4 openbabel
export BABEL_INCLUDEDIR=/usr/include/openbabel-2.0/openbabel
export BABEL_LIBDIR=/usr/lib/openbabel/2.3.1/
export BABEL_DATADIR=/usr/share/openbabel/openbabel/2.3.1/
To compile under Ubunt 12.04
sudo apt-get install libopenbabel-dev libopenbabel4 openbabel
export BABEL_INCLUDEDIR=/usr/include/openbabel-2.0/openbabel
export BABEL_LIBDIR=/usr/lib/openbabel/2.3.1/
export BABEL_DATADIR=/usr/share/openbabel/openbabel/2.3.1/