| qdipsim.f | The program to compute the similarity matrix for a set of proteins. The coordinates of the proteins should reside in the current directory and their file names should be listed in the file "names". It finds charged residues, assigns formal charges assuming standard protonation states at pH 7, computes monopole and dipole moments and writes the similarity index as described in the paper 1 |
| 2potsim_noskin.f | The program to compute the similarity index of 2 proteins, the interaction properties of which are given in the files "grd1.grd" and "grd2.grd" in UHBD format, using all grid points outside the protein |
| 2potsim_skin.f | The program to compute the similarity index of 2 proteins, the interaction properties of which are given in the files "grd1.grd" and "grd2.grd" in UHBD format and the coordinates of which are given in the files "pdb1.pdb" and "pdb2.pdb". The program constructs the "skin" around both proteins, and uses only the grid points within this "skin". The "skin" is constructed at the distance "probe" from the van der Waals surfaces of proteins and has a thickness given by the variable "skin". These 2 parameters are read from the file "probe.and.skin". the default values are 3 and 4 A, respectively |
| 2potsim_skin_parts.f | The same as 2potsim_skin.f, but will compute the similarity of potentials only around directions specified in the file "parts" |
| mkkin.f | Reads the similarity matrix, computes distances between proteins as defined by their similarity index, and represents proteins as points in 3D space, such that pairwise distances between each pair of proteins are represented by distances between corresponding points |
| mkdismx.f | Converts similarity matrix to distance matrix |
| ccenter.f | Auxiliary program to compute the geometric center of all atoms in a pdb file |
| mkcenter.f | Auxiliary program to compute the average center of proteins from the outputs of the previous program, which is then used as the center for all electrostatic potential grids. Also shows dispersion of the centers, which may be used as a check of the degree of superposition of proteins |
| whatif2uhbd.f | The program to convert the WHATIF output file of protein coordinates to the format readable by UHBD. Note that the current version treats correctly only one-chain proteins, i.e. you need to do modifications if proteins having more than one chain need to be analysed (read more). |
| modeller2grin.f | The program to rename some atom names from MODELLER output to the names readable by the program grin of GRID |
| mk_gridin.f | Writes input file for GRID, using information about the average center from the output of the mkcenter.f and the probe name given as a command line argument |
Data files:
| addh_in | input command script for WHATIF to add hydrogens to pdb file |
| grin.in | input file for executable "grin" of GRID |
| grub.dat | data file used by GRID, from GRID distribution |
| parts | example of the file "parts" for 2potsim_skin_parts |
| qtable.dat | data file for UHBD, used to assign OPLS charge+radius parameters to atoms |
| qtable_f.dat | data file for UHBD, which assigns partial charges only to charged residue side-chains |
| uhbd.in | input command script for UHBD |
Scripts:
| do_pipsa | the main script which executes the other scripts in the proper directories |
| do_pipsa_analyt | the script to add polar hydrogens to pdb coordinate files |
| do_pipsa_UHBD | adds polar hydrogens to pdb coordinate files using WHATIF, computes electrostatic potential grids using UHBD, and runs similarity calculations on these grids |
| do_pipsa_GRID | computes interaction field grids using GRID and runs similarity calculations on these grids |
Note that the program (whatif2uhbd), post-processing
the pdb files prepared by WHATIF to the format readable by
UHBD, can only treat one-chain proteins, and you need modifications
of the script of adding H-atoms when dealing
with many-chain proteins. Alternatively, the step of adding
hydrogens may be skipped (replaced by copying files to
whatif/ directory) and UHBD computations may be carried out on pdb
files without hydrogens, in such case the
data file qtable_f.dat should be used instead
of qtable.dat .
Razif Gabdoulline , January 2000