BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 Figure 3 Three individual multiple sequence alignments of the nine repeats of the PGIP molecules. A, B and C show the multiple sequence alignments with the nine LRR repeats (R1-R9) for PvPGIP1, PvPGIP2 and GmPGIP3 respectively. The black coloured positions in A and B correspond to the residues that differ between PvPGIP1 and PvPGIP2 while grey coloured positions in B and C highlight the varying residues between PvPGIP2 and GmPGIP3. The varying residue positions that are in bold are considered as insertion. or variable part of the repeat or in the non-LRR region, black, grey and hatched vertical bars are respectively used in Figure 2A and 2C. In both these proteins (PvPGIP1 and GmPGIP3 that share a similarity of 87%), most of the changes that fall in the LRR region (black bars in Figure 2) are either an allowed variant of the conserved position (L or C or N) or is any amino acid in the X position of the conserved region or is an amino acid belonging to the variable region of the repeat (grey bars). One exception is the variation in the conserved position N of R1 in PvPGIP1 (Figure 3A) where the replacing amino acid H is not an allowed variant. Regarding the variations in the non-LRR region, Additional file 1 points out that whereas PvPGIP1 and PvPGIP2 share 50% of the changes in this region, GmPGIP3 and PvPGIP2 show only 15% of it. This could probably indicate specific regions of importance in PGIPs for the introduction of variation for recognition of different enzymes from pathogens. Modelling The crystal structure of PvPGIP2 (1OGQ) being available and also since PvPGIP1 and PvPGIP2 as well as PvPGIP2 and GmPGIP3 share high percentage of sequence similarity, homology models of PvPGIP1 and GmPGIP3 were built using PvPGIP2 as template. One model each for PvPGIP1 and GmPGIP3 were selected using PRO- CHECK [25]. In each case, the model that was chosen supported the following criteria: (i) more number of residues in the core region (ii) no residues in the disallowed region These models of PvPGIP1 and GmPGIP3 were solvated in water and were subjected to energy minimization followed by molecular dynamics simulation of 1 ns. A similar scheme of equilibration was taken up for the crystal structure of PvPGIP2. RMSD of the equilibrated structures of PvPGIP1 and GmPGIP3 were calculated with respect to the equilibrated structure of PvPGIP2 and was found to be 1.45Å and 1.66Å respectively. Docking We used GRAMM-X [26] for docking three pairs of proteins in order to unveil the mode of interaction within and across each pair. This docking program executes a rigid-body search using Fast Fourier Transform (FFT) correlation with simplified geometry employing shape complementarity and hydrophobicity in the scoring function. In this study we have used GRAMM-X as a protein-protein docking program as it extends the GRAMM Fast Fourier Transformation methodology by applying smoothed Lennard-Jones potential, refinement stage and knowledge-based scoring, thus giving rise to best surface match. The output of GRAMM-X is a PDB file containing the structures of ten models ranked as the most probable prediction candidate, according to the scoring function used. The cell-wall degrading enzyme PG, from the fungus Fusarium moniliforme was common Page 5 of 12 (page number not for citation purposes)