The document discusses the features and requirements of AutoDock 4 and AutoDock Vina, highlighting their scoring functions, optimization algorithms, and execution methods. It details the necessary input file formats and the types of output generated. Additionally, the document provides references for further information and tutorials related to the software.

1. AUTODOCK 4 AUTODOCK VINA
1. Use lga based scoring function. 1. Use local search global optimizer
2. Work on genetic and Lamarckian
algorithm
2. Use Broyden–Fletcher–Goldfarb–
Shanno algorithm.
3. Require multiple steps for execution. 3. Work on single threaded execution
method.
4. Docking score is calculated by default
scoring function.
4. Same
5. We can set lga parameters. 5. Not required.
6. File format input require- .pdb, .pdbqt,
autodock.exe and autogrid.exe binaries.
6. .pdb. .pdbqt, config.txt and vina.exe
required.
7. Output generated- .gpf, .glg, .dpf and
.dlg.
7. grid.txt ,output.pdbqt and log.txt
generated.

2. REFERENCES:-
1. https://www.mdpi.com/2076-3417/9/21/4538/htm
2. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/
4. http://vina.scripps.edu/download.html (to download vina)
5. https://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp01555g#!divAbstract
6. https://link.springer.com/article/10.1007%2Fs40484-019-0172-y
7. https://www.researchgate.net/post/What_algorithm_does_Autodock_Vina_use
8. https://youtu.be/k6tqCeDIwEk ( autodock 4 tutorial)
9. https://youtu.be/Sux91FJ3Xe8 , https://youtu.be/vU2aNuP3Y8I ( autodock vina tutorial)
10. http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ (autodock 4
download)
11. http://mgltools.scripps.edu/ (mgl tools download)