title: Software Infrastructure for Computer-aided Drug Discovery and Development, a Practical Example with Guidelines.
abstract: In the field of Computer-Aided Drug Discovery and Development (CADDD) the proper software infrastructure is essential for everyday investigations. The creation of such an environment should be carefully planned and implemented with certain features in order to be productive and efficient. Here we describe a solution to integrate standard computational services into a functional unit that empowers modelling applications for drug discovery. This system allows users with various level of expertise to run in silico experiments automatically and without the burden of file formatting for different software, managing the actual computation, keeping track of the activities and graphical rendering of the structural outcomes. To showcase the potential of this approach, performances of five different docking programs on an Hiv-1 protease test set are presented.
authors.affiliation: Drug Discovery Program, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy. loris.moretti.dc@gmail.com.|Nuevolution A/S, Rønnegade 8, DK-2100, Copenhagen, Denmark. loris.moretti.dc@gmail.com.
authors.forename: Loris
authors.initials: L
authors.lastname: Moretti
authors.affiliation: Drug Discovery Program, Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy.|Experimental Therapeutics Unit, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Sartori
mesh_terms: D019380:Anti-HIV Agents / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D017076:Computer-Aided Design; D003201:Computers; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods*; D012984:Software
chemical_list: D019380:Anti-HIV Agents
keywords: Computer-Aided Drug Discovery and Development; computational infrastructure; docking; good CADDD practices; molecular modelling