AutoDock Vina
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AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.
Features :
Accuracy
AutoDock Vina significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4, judging by our tests on the training set used in AutoDock 4 development.[*]
Additionally and independently, AutoDock Vina has been tested against a virtual screening benchmark called the Directory of Useful Decoys by the Watowich group, and was found to be "a strong competitor against the other programs, and at the top of the pack in many cases". It should be noted that all six of the other docking programs, to which it was compared, are distributed commercially.
AutoDock Tools Compatibility
For its input and output, Vina uses the same PDBQT molecular structure file format used by AutoDock. PDBQT files can be generated (interactively or in batch mode) and viewed using MGLTools. Other files, such as the AutoDock and AutoGrid parameter files (GPF, DPF) and grid map files are not needed.
Ease of Use
Vina's design philosophy is not to require the user to understand its implementation details, tweak obscure search parameters, cluster results or know advanced algebra (quaternions). All that is required is the structures of the molecules being docked and the specification of the search space including the binding site. Calculating grid maps and assigning atom charges is not needed. The usage summary can be printed with "vina --help". The summary automatically remains in sync with the possible usage scenarios.
Implementation Quality
By design, the results should not have a statistical bias related to the conformation of the input structure.
Attention is paid to checking the syntactic correctness of the input and reporting errors to the user in a lucid manner.
The invariance of the covalent bond lengths is automatically verified in the output structures.
Vina avoids imposing artificial restrictions, such as the number of atoms in the input, the number of torsions, the size of the search space, the exhaustiveness of the search, etc.
Flexible Side Chains
Like in AutoDock 4, some receptor side chains can be chosen to be treated as flexible during docking.
Speed
AutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude.[*]
Multiple CPUs/Cores
Vina can take advantage of multiple CPUs or CPU cores on your system to significantly shorten its running time.
Reproducibility
Given the same binary version of the program, the same input, options and random seed, the results should be reproducible with any value of "cpu".
Free download from Shareware Connection - AutoDock Vina is a new open-source program for drug discovery
Version: 1.1.2 | Size: 501 KB | Platform: WinOther
Released Date: | Rating: 0 | Title: AutoDock Vina
Author Url: http://vina.scripps.edu
Program Info Url: http://vina.scripps.edu
Download Url: http://vina.scripps.edu/download/autodock_vina_1_1_2_win32.msi
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Shareware Connection periodically updates pricing and software information of 'AutoDock Vina' from company source 'Oleg Trott' , so some information may be slightly out-of-date. You should confirm all information before relying on it. Software piracy is theft, Using 'AutoDock Vina' crack, password, serial numbers, registration codes, key generators is illegal and prevent future development of AutoDock Vina.
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