Research, Heidelberg, Germany
EMBL, Heidelberg, Germany
PIPSA may be used to compute and analyze the pairwise similarity of 3D interaction property fields for a set of proteins.
It is first described in:
N. Blomberg, R.R.
Gabdoulline, M. Nilges and R. C. Wade.
Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.
Proteins: Str., Function and Genetics, 37:379-387 (1999).
are computed from the 3D coordinates of a set of superimposed proteins.
Similarity indices can be computed and analysed for three different types of property:
1. The monopole and dipole moments of proteins, which are analytically computed descriptors for their electrostatic potentials;
2. Electrostatic potentials obtained by numerically solving the finite-difference Poisson-Boltzmann equation (FDPBE) on a grid;
3. Other types of interaction property, e.g. probe interaction energies evaluated with the GRID program, that can be mapped on to a grid.
PIPSA produces a matrix of pairwise similarity indices for each protein interaction property. This matrix is converted into a distance matrix which may be used for clustering or visualization.
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