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  1. autodock-vina.readthedocs.io › en › latestFrequently Asked Questions — Autodock Vina 1.2.0 documentation

    This is probably because you intended to specify the search space sizes in “grid points” (0.375 Angstrom), as in AutoDock 4. The AutoDock Vina search space sizes are given in Angstroms instead. If you really intended to use an unusually large search space, you can ignore this warning, but note that the search algorithm’s job may be harder.

    • Installation

      Create a dedicated environment for AutoDock Vina. This...

    • Changes

      Autodock Vina. Changes; View page source; Changes 1.2.0...

    • Citations

      AutoDock Vina AutoDock Vina is a scientific software that is...

    • Basic Docking

      The command specifies that the provided 1iep_receptorH.pdb...

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  3. vina.scripps.edu › manualManual - AutoDock Vina

    What is the difference between AutoDock Vina and AutoDock 4? AutoDock 4 (and previous versions) and AutoDock Vina were both developed in the Molecular Graphics Lab at The Scripps Research Institute. AutoDock Vina inherits some of the ideas and approaches of AutoDock 4, such as treating docking as a stochastic global opimization of the scoring ...

  4. www.researchgate.net › post › What_is_the_majorWhat is the major difference/s between Autodock 4.0 and ...

    Feb 19, 2017 · The major difference is the scoring function. In Autodock 4 the scoring function is based on the AMBER force field and in Autodock Vina it is a hybrid scoring function (empirical + knowledge-based ...

  5. www.blopig.com › 01 › autodock-4-and-autodock-vinaAutoDock 4 and AutoDock Vina | Oxford Protein Informatics Group

    These protocols corresponded to 250k evals, 2.5m evals and 25m evals for AutoDock 4; and exhaustiveness values of 8, 56, and 400 for AutoDock Vina. No surprises, they reported that AutoDock Vina was faster than AutoDock 4. But AutoDock 4 showed better performance, in terms of Pearson correlation coefficient of the predicted binding affinity ...

  6. indico4.twgrid.org › AutoDock4andAutoDockVinaHands-on tutorials of AutoDock 4 and AutoDock Vina

    pdb2pqr. pdb2pqr prepares structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files. PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.

  7. sebastianraschka.com › Articles › 2014_autodockMolecular docking, estimating free energies of binding, and ...

    Jun 26, 2014 · Vina is considered to be the successor of AutoDock4.2 and comes with a new knowledge-based, statistical scoring function that replaces the semiempirical force field of AutoDock. The advantages of Vina over AutoDock4.2 are its improved prediction accuracy and speed, which is not only due to the simplification of the scoring function, but also due to the capability of multi-threading in presence of multiple CPU cores.

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  9. autodock-vina.readthedocs.io › en › latestAbout AutoDock Vina — Autodock Vina 1.2.0 documentation

    AutoDock Vina (Vina) is one of the docking engines in the AutoDock Suite, together with AutoDock4 (AD4), AutoDockGPU, AutoDockFR, and AutoDock-CrankPep, and arguably among the most widely used and successful docking engines. The reasons for this success are mostly due to its ease of use and its speed (up to 100x faster than AD4), when compared ...