Protein Interaction Property Similarity Analysis

Installation of PIPSA 3.0
(Protein Interaction Property Similarity Analysis)

The PIPSA software distribution consist of a set of fortran 77 programs, accompanying data files and Unix shell scripts to analyse interaction field grids.
Additionally, several other licensed programs may be be required, depending on the type of the similarity calculation performed.

To install, uncompress and untar the PIPSA distribution package ( `gunzip -c pipsa.tar.gz | tar xvf -` ).
This will give you the PIPSA distribution directory (`pipsa/`) with the following subdirectories:
aux/ - Auxiliary programs and scripts that can be used for special purposes
bin/ - Linux executables of pipsa programs compiled using g77
data/ - Data files needed for PIPSA
doc/ - Documentation
src/ - Fortran source files of PIPSA programs
scr/ - PIPSA example shell scripts
exa/ - PIPSA usage examples

The PIPSA scripts can be used under any Unix environment; the distributed executables are compiled under Linux using g77.
The programs might need to be recompiled in order to run under your unix system or in order to optimize their performance. To do this, remove all files from the bin/ subdirectory, go to src/ subdirectory, edit (if needed) the Makefile to adjust your compiler options and type "make all". This will generate new executables in the bin/ subdirectory.

Programs to use in conjunction with PIPSA
The program WHATIF 1 by G. Vriend can be used to add polar hydrogens to pdb coordinates of proteins, and then the program UHBD 2 used to compute electrostatic potentials of proteins.
- Alternatively, the PDB2PQR 3 web service can be used to add hydrogens and assign parameters and the program APBS 4 by N. Baker may be used to compute electrostatic potentials of proteins.
- The program GRID 5 by P.Goodford can be used to compute the grids of probe interaction fields.
- The program NMRCLUST 6 by M. Sutcliffe is used to check clustering of the proteins based on pairwise distances derived from similarity matrices.
- The program MAGE 7 by D. Richardson is used to visualize the distribution and clustering of proteins in 3 dimensions based on the pairwise similarity measures.
- The program Phylip 8 by J. Felsenstein is used to derive phylogeny trees from pairwise similarities of proteins.

The following table lists additional programs required to compute and vizualize similarity properties (free for academia programs in green):

Similarity estimate | Analytical electrostatic properties | UHBD computed electrostatic potentials | APBS computed electrostatic potentials | GRID computed interaction fields
Required programs (computation) | - | WHATIF, UHBD | PDB2PQR, APBS | grin, grid, k2a
Required programs (vizualization) | MAGE, NMRCLUST, Phylip | MAGE, NMRCLUST, Phylip | MAGE, NMRCLUST, Phylip | MAGE, NMRCLUST, Phylip

References

1 G. Vriend. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. (1990) 8, 52-56. http://swift.cmbi.kun.nl/whatif/

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. http://adrik.bchs.uh.edu/uhbd.html
3 Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research (2004) 32, W665-W667. http://nbcr.sdsc.edu/pdb2pqr/

4 Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA (2001) 98, 10037-10041. http://agave.wustl.edu/apbs/

5 Goodford, P. J. J. Med. Chem. (1985) 28, 849. http://www.moldiscovery.com/soft_grid.php

6 L.A. Kelley, S.P. Gardner and M.J. Sutcliffe. An Automated Approach For Clustering An Ensemble Of NMR-Derived Protein Structures Into Conformationally-Related Subfamilies. Protein Engineering (1996) 9, 1063-1065. http://neon.chem.le.ac.uk/nmrclust/

7 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. http://kinemage.biochem.duke.edu/

8 Felsenstein, J. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics (1989) 5: 164-166. http://evolution.genetics.washington.edu/phylip.html

Razif Gabdoulline, 2007