Binary builds do not require python or numpy be installed to use. Everything needed to run PDB2PQR is included. Just unpack and use.
In Windows the executable file is called "pdb2pqr.exe".
In OSX and Linux the executable is called "pdb2pqr" and should already have the executable flag set.
OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.
Linux binaries require CentOS 6 or newer and have been tested on Ubuntu 12.04 LTS and Linux Mint 13. If you are running 64-bit Linux use the 64-bit libraries. In some cases the needed 32-bit system libraries will not be installed on a 64-bit system.
Windows binaries are 32 bit and were built and tested on Windows 7 64-bit but should work on Windows XP, Vista, and 8 both 32 and 64-bit systems.
Instructions on how to create a binary build from source are found in INSTALL.md in the source tarball.