Frequently asked questions for PIPSA
(Protein Interaction Property Similarity Analysis)
1. I have pdb files of my
proteins, but PIPSA fails to proceed them, what is wrong ?
Pdb files should prepared before running PIPSA. Depending
which interaction field will be compared, prepared versions of pdb
files should be readable by APBS, UHBD or GRID. Instructions for
APBS and UHBD are given in usage example page example.html#pdb . Changes needed for
GRID are described in GRID
2. PIPSA did not
superpose my proteins
It should not do this either. You have to take care about
before running PIPSA. There are many protein superposition tools
that can be used for this purpose. The question "how to
superpose?" is related to the question "which part of proteins should
be compared?". PIPSA can be used for any type of superposition of
the regions to be compared (this is not necessarily complete surfaces
of homologous proteins, can be similar active sites of otherwise
structurally different enzymes).
3. How do I change ionic
strength value to 150 mM from default 50 mM ?
Read the user guide calculation parameter section usrguide.html#param . You should
modify APBS (or UHBD) preparation script: make a local copy from distribution version scr/do_pipsa_APBS_prep
(or scr/do_pipsa_UHBD_pre, modify,
and run (this can be done from any directory because directory
locations are given as input parameters for PIPSA scripts)
Alternative is to modify apbs.in (or uhbd.in) files after the
preparation script was already executed and input file for APBS (or
UHBD) are created in apbs (or uhbd) work directory. This input
file, apbs.in (or uhbd.in), should be edited changing ionic strength
assignment. This way is useful in changing other interaction
field calculation parameters locally (not changing scripts and template
files in PIPSA distribution directory).
4. I have more than 999
proteins and PIPSA does not work
Read the user guide, calculation parameter section usrguide.html#param . In this case you
have to change nprmx from default 999 to
a larger value and recompile PIPSA
programs (or at least the following programs: mkapbsin, mkdismx,
Changing namx to a larger value and
recompiling ccenter is needed if your proteins have more than 9999
5. I have many proteins
and similarity calculations take ages
Use parallel version of PIPSA
Try to allocate grid and pdb files on the disk with faster access
- PIPSA needs comparable times both for calculations and reading in
data files - this is increasingly important for larger grid files.
6. I want to change one
protein pdb file, should I re-calculate all pairwise similarities now ?
It is possible first remove the protein to be modified from the
set of analysed proteins, using the script scr/do_pipsa_rem1 and add it
again using the script scr/do_pipsa_add1. First step will only remove
the protein name from the list of proteins and the entries related to
it in similarity matrix file (sims.log), so that changing of pdb and
grid files can be made before or after this step. The second step
will use new (if updated) pdb and grid files and do calculations only
for pairs involving the added protein.
Note that this method may give the analysis results different
from the case when the analysis is done from the very
beginning. First, the name of the replaced protein will
disappear from its original location and appear at the end of the list
of proteins. Second, old center for grids will be used for
calculations, while this center will be recalculated and may differ
from original center if all calculations are repeated.
7. How do I run PIPSA on
WindowsXP / MacOSX ?
Running PIPSA on OS-s rather than Linux is not supported, but it
is possible. You have to be able (a) to compile fortran programs
and (b) to
run pipsa shell scripts. (a) can be done using GNU
compilers , a special attention to be paid -static option of
compilation (at least for npotsim.f, n1potsim.f, m1potsim.f). (b)
is straightforward under MacOS, can be universally solved by cygwin inder Windows, or by
modifying pipsa scripts to run under respective OS.
8. Why there are 2 versions
mkapbsin.f and mkapbsin-apbs-ot-0.3.2.f ?
Second program supposed to be used (instead of mkapbsin) with
APBS versions older than 0.3.2. This is caused by the difference
defining UHBD format output grid origin in versions before and after
9. I have electrostatic
potentials as DELPHI grid files, can I compare them with PIPSA ?
You have to convert them to UHBD grid format.
The same applies to any interaction fields calculated with other
programs (i.e. conversion to UHBD grid format to be done before using
10. How do I compare one part of
my protein with its another part ?
You have to prepare 2 pdb files, the first for one part and the
second for another part, superpose them so that the parts to be
compared are located on the same place in 3D, and run PIPSA on these 2
proteins. For example, if you want to compare 2 monomers of a
dimeric protein, the monomers should be extracted to 2 pdb files,
these 2 pdb files should be superposed based on the sequence alignment,
and PIPSA should be run using these 2 superposed pdb files.
11. Can I use PIPSA for
non-protein molecules ?
Yes, you can, as soon as these molecules are superposed and their
interaction fields are calculated and stored in UHBD grid format.
12. I can not get any
correlation between the interaction fields and experimental kinetic
parameters in qPIPSA analysis, what is wrong ?
According to qPIPSA methodology (here), the absence of correlation
does not necessarily means that something is going wrong.
Presence of correlations needs many assumptions to hold, such as:
Kinetic parameter measurement conditions should be consistent
with the conditions of structural modeling. Conditions known to
influence correlations are ionic strength and pH of the solvent.
Either experiments under the same environmental conditions should be
chosen for qPIPSA, or modeling should be adapted to each specific
The proteins structures used in the analysis should be relevant
for the rate-determining catalytic step. Proteins may adopt
multiple conformations. Sometimes it may be
necessary to do calculations with more than one conformation, e.g. with
open and closed forms of an enzyme active site. If one of these gives
MIFs that correlate better with known kinetic parameters, this provides
somemechanistic information about the determinants of the kinetic
The region, over which interaction fields are compared, should
be relevant for the kinetics. Calculations can be done for a
number of regions. For TPIs, the best
correlation with kinetic parameters was obtained for different regions
for kcat/Km values and Km values. This again provides some mechanistic
information on the parameter determinants.
The method is most suitable when the rate-determining step is
mechanistically the same across the set of protein structures compared.
An outlier might be mechanistically different, but if there is wide
mechanistic variation in the dataset, the comparative approach cannot
be expected to work.
Molecular dynamics are not currently considered in the approach
they alter the protein structures in different ways across the dataset
they will adversely affect the value of the interaction field
13. What are the two ways of
running PIPSA ?
The first is to use prepared scripts (from subdirectory scr/ of
pipsa distribution) combining them to accomplish the task you
need. These scripts are designed to perform specific tasks taking
as a parameter the data and executable locations. You may need to
have local modified copies of these scripts to suit your tasks.
The second is to write scripts invoking basic programs, like
n*potsim, 2potsim from pipsa's bin/ subdirectory.