David W. Gohara, Ph.D.

Vale is an application for the prediction of ion binding sites in proteins. The program takes as input a PDB file and scans the structure for coordinating geometry to assess if the 3D configuration of atoms is consistent with that of known ion binding site configurations. Vale is available as FORTRAN source code and can be compiled with either open source or commercial software compilers. Instructions for compiling with the Intel FORTRAN compiler and gfortran are given below.

ifort -O3 vale.f -o vale
gfortran -O3 vale_g77.f -o vale


Please see the attached manuscript for additional information.

WASP is used for assessing water molecule assignment in protein structures determined by X-ray crystallography. Given a PDB file, with waters, each water molecule is analyzed in the context of its surrounding atoms. Water molecules matching a specific coordination geometry and valence are then output as potential candidates for re-evaluation as possible cations. Binaries of OS X and 64-bit Linux are provided, as well as source code. The software can be built for other platforms using a FORTRAN compiler. Instructions for building WASP from source using Intel compilers or gfortran are given below.

ifort -O3 wasp.f -o wasp
gfortran -O3 wasp_g77.f -o wasp


Please see the attached manuscript for additional information.