BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 Determination of ionic interaction and hydrogen bonding patterns in the complexes The Protein Interaction Calculator (PIC) [28] was used to detect the ionic interaction between the proteins in the three complexes. Electrostatic surface potential Adaptive Poisson-Boltzmann Solver (APBS) is a software package for the numerical solution of the Poisson- Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interac- tions between molecular solutes in salty, aqueous media. The colour coded electrostatic surface potential was drawn using the APBS (Adaptive Poisson-Boltzmann Solver) package [29] within PYMOL 0.99rc6 [41] for the three PGIP molecules, the PG molecule and the three complexes. Electrostatic surface potential was also generated for a model where a single mutation was carried out on PvPGIP2 (Q224K) by WHAT IF [30,40] using the APBS package [29]. List of abbreviations used LRR: Leucine-rich repeat; PGIP: PolyGalacturonase Inhi- biting Protein; pgip: PolyGalacturonase Inhibiting Pro- tein coding gene; PG: PolyGalacturonase; PvPGIP: Phaseolus vulgaris PolyGalacturonase Inhibiting Protein; GmPGIP: Glycine max PolyGalacturonase Inhibiting Protein; FmPG: Fusarium moniliforme PolyGalacturonase; PAMP: pathogen associated molecular pattern; HGA: homogalacturonan; PS_LRR: plant specific Leucine-rich Repeats; SASA: Solvent Accessible Surface Area; APBS: Adaptive Poisson-Boltzmann Solver; PBE: Poisson-Boltz- mann equation; PIC: Protein Interaction Calculator. Competing interests The authors declare that they have no competing interests. Authors’ contributions Both AM and SB designed the plan of work and performed the analyses. HG participated in the devel- opment of the work. SB conceived of the study and coordinated the work. All authors read and approved the final manuscript. Note Other papers from the meeting have been published as part of BMC Bioinformatics Volume 10 Supplement 15, 2009: Eighth International Conference on Bioinfor- matics (InCoB2009): Bioinformatics, available online at http://www.biomedcentral.com/1471-2105/10? issue=S15. Additional material Additional file 1 Details of the distribution of the sequence variations in PvPGIP1 and GmPGIP3 with PvPGIP2 over the conserved and variable portion of the repeat and the non-LRR region. The table shows the distribution of the varying residues in PvPGIP1 and GmPGIP3 with PvPGIP2 in the LRRs and non-LRR regions. The changes that occur in the LRR region is either L/N/C of the conserved segment (LxxLxLxxNxL) or is x. They are denoted by cL, cN, cC and cX where X is any amino acid. Amino acid in the variable region of the LRR is denoted by v. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-S3-S19-S1.pdf] Additional file 2 Electrostatic surface potential of PvPGIP2 with a single mutation at 224. Q(224) of PvPGIP2 is mutated to K which is the residue found in PvPGIP1. The electrostatic surface potential changes considerably with a single mutation when compared to Figure 5B. Experimental studies on this single mutation have shown a 70% reduction in the inhibition ability of PvPGIP2. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-10-S3-S19-S2.pdf] Acknowledgements AM is grateful to Department of Biotechnology, Government of India for providing her with fellowship. The authors deeply acknowledge Dr. Ansuman Lahiri and Dr. Anindita Seal for their critical reading of the manuscript and useful discussion. 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