Polygalacturonases (PGs) hydrolyze the pectins present in the cell walls of higher plants. PGs prefer pectic acid rather than pectins as substrate and methylesterification of pectic acid is known to inhibit the activity of fungal PG. In order to identify the molecular basis of the differential specificity towards the substrates, octagalacturonic acid and its methylesterified derivative are flexibly docked with tomato PG and fungal PG. The substrate octagalacturonic acid is found to bind with the non-reducing end towards the N-terminus of PG whereas its methylesterified derivative binds in opposite direction with both the PGs. Both methylesterified derivative complexes did not show the catalytically important Asp residue in the interaction map suggesting strongly the inactiveness of the PGs with the methylesterified substrate. The tomato PG-octagalacturonic acid complex possesses stronger interaction when compared to its methylesterified substrate whereas it is the methylesterified substrate, which shows stronger interaction in the fungal PG explaining its inhibition mode. (c) 2006 Elsevier Ltd. All rights reserved.