Molecular Evaluation using Comparative Molecular Interaction Profile Analysis system

Comparative M olecularInteraction ProfileAnalysis system (CoM IPA) thatutilize virtualdocking study for comprehensive analysis of molecular interactions.The dockingengineuses AutoDock 3.0, which is widely used for docking evaluation of small molecule compound/protein complexes. By using pre-made grid maps for each receptor, the system can evaluate the possibility of these interactions faster.W e propose thatthe new concept of profiling be called interaction profiles (IPFs), which is a dataset of interaction energies. Conventionally, physical and chemical properties such as molecular weight, volume, and electric charge have been used to characterize small molecules.W e proposea new description factor,IPF which is valuable for directly comparing different molecularinteractions. Creating a new moleculardescription factorbased on theresultsofcomputationaldocking study willadd new dimensionsinmolecular evaluation.Wepropose a new molecular description factor analysis system named Comparative M olecular Interaction Profile Analysis system (CoM IPA) in which the AutoDock program is used for docking evaluation of small molecule compound-protein complexes. Interaction energiesare calculated,and the datasetsobtainedare named interaction profiles (IPFs). Using IPF as a scoring indicator,the system could bea powerfultool to cluster the interacting properties between small molecules and bio macromolecules such as ligand-receptor bindings. The system can use computational molecular docking results to explain biological events such as adverse drug reactions and possibly other unforeseen interactions caused by environmental hormones. We believe that the system has the potential to be a major stepping-stone for bridgingcomputationalscience andbiology. 2. M aterialsand M ethods Comparative M olecularInteraction ProfileAnalysis system (CoM IPA) is an application aimed to evaluatethe molecularinteractionsbetween asmall molecule compound and multiple proteins by dockinganalysis.The dockingengine ofCoM IPA