Dockomatic: An Emerging Resource to Manage Molecular Docking

Abstract

The application of computational modeling to rationally design drugs and characterize macro-biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. A limitation of AutoDock is the inability of a user to automatically create ligands and manage the input and output of data when dealing with large numbers of simulations; a problem that arises in High Throughput Virtual Screening (HTVS) or Inverse Virtual Screening (IVS). We have designed DockoMatic, a user friendly Graphical User Interface (GUI) application that constructs peptide-based ligands, integrates with the software program TreePack to create user defined peptide analogs, and automates the creation and management of AutoDock jobs for HTVS of ligand to receptor interactions. DockoMatic is a valuable tool for studying complex systems such as conotoxins, from the genus Conus, and their interactions with the well-characterized molecular receptor, Aplysia californica acetylcholine binding protein (Ac-AChBP)