Dockbox download

Note that a valid license of MOE is required. The former is intended to be used solely for docking and rescoring while the latter enables to analyze the results and to select the best pose s from a combination of scores or among different consensus docking schemes. The rundbx routine allows the user to dock and rescore a ligand to a protein target using multiple docking and scoring functions. When finished correcly, a rundbx job should have created a folder called poses containing all the poses generated by the different docking programs as specified in the INI configuration file.

Each pose is provided in a file with. Within the poses folder, a file called info. Below is an example of an info. No label for the binding site was specified as docking was performed on the same site. For example, if Autodock and Autodock Vina were used to dock on three different binding sites called site1, site2 and site3 see section Preparing the INI configuration file , then a total of six folders named autodock.

Besides one MOL2 file containing the ligand structure -l flag and one PDB file containing the receptor structure -r flag , running rundbx requires a configuration file -f flag that specifies all the parameters needed for the docking procedure.

Each section contains a certain number of keys which refer to specific options used; all keys after the section declaration are associated with that section. Below is an example of configuration file used to dock on two binding sites and rescore with DrugScoreX dsx , Autodock and Autodock Vina. Below is a list of all the options per software that can be specified in the configuration file.

Note 3 : As is usually the case for Autodock, non polar hydrogens in the ligand structure are removed prior to docking in order to properly use the Autodock force field. Once the docking has been performed, nonpolar hydrogens are reattributed in a way consistent with the input structure.

Unless the minimize option in the configuration file is set to yes , no minimization is performed on those hydrogens. Note 4 Final poses are extracted from the.

Note 2 : As is usually the case for Autodock Vina, non polar hydrogens in the ligand structure are removed prior to docking in order to properly use the Autodock force field. Below is an example of configuration file that can be used as an input of rundbx. The docking procedure is carried out on a single binding site specied as a box with dimensions Below is another example of configuration file for rundbx used to dock on two binding sites and rescore with DrugScoreX dsx , Autodock and Autodock Vina.

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