The program suite presented here should be used under the unix environment. This applies to the unix specific scripts, as well as to the programs, which have only been tested under unix (SGI IRIX 6.5). The program WHATIF 1 by G. Vriend is used to add polar hydrogens to pdb coordinates of proteins. The program UHBD2is required to compute electrostatic potentials of proteins. Additionally, the program GRID3 by P.Goodford is used to compute the grids of probe interaction fields. The program NMRCLUST4 by M. Sutcliffe is used to check clustering of the proteins based on pairwise distances derived from similarity matrices. The program MAGE5 by D. Richardson is used to visualize the distribution and clustering of proteins in 3 dimensions based on the pairwise similarity measures. The following table lists additional programs required to compute and vizualize similarity properties:
| Similarity estimate | Analytical | UHBD | GRID |
| Required programs (computation) | - | UHBD,WHATIF | grin,grid |
| Required programs (vizualization) | MAGE,NMRCLUST | MAGE,NMRCLUST | MAGE,NMRCLUST |
Executables were compiled on an SGI O2 workstation running IRIX 6.5.
References to programs:
1 WHAT
IF: A molecular modeling and drug design program. G.Vriend, J.
Mol. Graph. (1990) 8, 52-56.
2 Madura,J.D.; Briggs,J.M.; Wade,R.C.; Davis,M.E.;
Luty,B.A.; Ilin,A.; Antosiewicz,J.; Gilson,M.K.; Bagheri,B.; Scott, L.R.
and McCammon,J.A. Electrostatics and Diffusion of Molecules in Solution:
Simulations with the University
of Houston Brownian Dynamics Program. Comp. Phys. Comm. (1995)
91, 57-95.
3 Goodford, P. J., J. Med. Chem.,
28 (1985) 849.
4 Lawrence A. Kelley, Stephen P. Gardner
and Michael J. Sutcliffe. An Automated Approach For Clustering
An Ensemble Of NMR-Derived Protein Structures Into Conformationally-Related
Subfamilies. Protein Engineering 9, 1063-1065(1996).
5 MAGE:
copyright © 1998 by David C. Richardson, Little River Institute, 5820
Old Stony Way, Durham NC 27705; dcr@kinemage.biochem.duke.edu; Biochemistry
Dept., Duke University, North Carolina 27710, USA
Razif Gabdoulline , January 2000