Dockres: a computer program that analyzes the output of virtual screening of small molecules

Dockres and some of its supporting utilities are written Fortran-77; other utilities are written as C-shell scripts. They support the parallel execution of the screening. The current implementation of the program handles virtual screening with Autodock-3 and Autodock-4, but can be extended to work with the output of other programs.Analysis of virtual screening by Dockres led to both active and selective lead compounds.Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere.Virtual screening of small molecules is a widely used in-silico technique as an initial step towards development of selective chemical ligands that functionally modulate a target protein [1-3]. Such screening typically involves minimization of a scoring function calculated at atomic-scale resolution. Employing computationally efficient algorithms allows screening of a large chemical library. Since the 'scoring-function landscape' is highly nonlinear, that would there are require repetition of the minimization several hundred times. This means that a single screen of a chemical library will generate a large number of complexes - described as 'poses' - whose visual examination is almost impossible for all practical purposes. This note describes a computer program that is designed to sort and filter a large set of poses by various selection criteria and extract the filtered complexes.Dockres, written in Fortran-77, scans the output files of Autodock-3 or Autodock-4 [4] resulting from screening of a library of chemical ligands and extracts the docked poses and their calculated scores. From the coordinates of a macromolecule (target) the environment of the docked poses can be established.There is an option to adjust the calculated free energy score with a contribution based on the multiplicity (m) of each pose [5]:The extracted poses are sorted by their scores calculated by Autodock. Figure 1 shows a typical record descri