Here, we use the abbreviation ADV, next to ADT. ADV and ADT were developed at the same academic group where Autodock4 ( AD4) was created, what may explain the word creation of VINA as an acronym for “Vina Is Not Autodock.” Other authors cite it as VINA. MGL tools- ADT-offer the possibility for ADV users to manipulate and visualize input and output data. Versions for three operating systems exist: MS-Windows, Linux, or MAC OS X. It can be installed on any desktop or laptop computer. So, it has to be downloaded first from the official web page. Two more programs can be helpful to prepare targets and ligands, namely proteins and small organic compounds: (3) a protein-specific tool box named Swiss PDB Viewer (SPDBV) and (4) Vega ZZ, which is a versatile molecular modeling program. (2) Input and output data of ADV can be generated and visualized by Autodock Tools (ADT) from the same academic site (AKA MGL-Tools). Together they carry out the tasks to input data, process docking, and analyze the output data: (1) Autodock Vina (ADV) is a popular docking program. Four programs are proposed because they all can be installed together under the same operating system on a computer, namely MS-Windows. Hence, a personal choice had to be made by combining popular programs for beginners to prepare molecular input data, run docking, and analyze the output. #Autodock 4.2 for mac os for freeIt lies beyond the scope of this book chapter to provide an exhaustive synopsis about computational tools that are available for free academic or private use, for instance, HADDOCK ( Dominguez et al., 2003), Chimera X ( Goddard et al., 2018), or web-based SwissDock ( Grosdidier et al., 2011), just to name three of them. Thomas Scior, in Molecular Docking for Computer-Aided Drug Design, 2021 2 Selecting the Docking Program and Associated Tools
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