AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4.

ABSTRACT: AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-targe

SUBMITTER: Valdes-Tresanco MS 

PROVIDER: S-EPMC7493944 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature