1. INTRODUCTION - Valdes-Tresanco-MS/AMDock-win GitHub Wiki
Here we introduce a manual showing all the functionalities of AMDock program. AMDock is a GUI program that assists docking runs with AutoDock Vina and AutoDock4 (including AutoDock4Zn force field for zinc-containing metalloproteins). The program includes: preparation of protein and ligand input files, the definition of a proper search space and docking run itself. There are multiple options to perform these tasks. That way, the user will be free to choose how automatic the docking run will be. Several programs are used and their functionalities on the AMDock context are explained across the manual. However, other applications of these programs are omitted here. All information about these programs can be reviewed in:
AutoDock Vina 1.2.1:
Manual: http://vina.scripps.edu/manual.html
Original Publication: Trott, O., Olson, A. J. (2010) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem, 31: 455-461.
AutoDock 4.2.6:
Manual: http://autodock.scripps.edu/faqs-help/manual/autodock-4-2-user-guide
Original Publication: Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem, 30: 2785-2791.
AutoDock4Zn Force Field:
Manual: http://mgldev.scripps.edu/AutoDockZN/AutoDockZN_userguide.pdf
Original Publication: Santos-Martins, D., Forli, S., João Ramos, M., Olson, A. J. (2014) AutoDock4Zn: an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Info Model, 54: 2371-2379.
Open Babel 2.4.1:
Manual: http://openbabel.org/docs/dev/OpenBabel.pdf
Original Publication: O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., Hutchison, G. R. (2011) Open Babel: An open chemical toolbox. J Cheminf, 3: 33.
PDB2PQR 2.1:
Manual: http://www.ics.uci.edu/~dock/pdb2pqr/userguide.html
Original Publication: Dolinsky, T. J., Nielsen, J. E., McCammon, J. A., Baker, N. A. (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32: W665-7.
AutoDockTools Module 1.5.7:
Manual: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools
Original Publication: Sanner, M. F. (1999) Python: A Programming Language for Software Integration and Development. J Mol Graphics Mod, 17: 57-61
AutoLigand:
Manual: http://autodock.scripps.edu/faqs-help/tutorial/using-autoligand-with-autodocktools
Original Publication: Harris, R., Olson, A., Goodsell, D. (2008) Automated prediction of ligand-binding sites in proteins. Proteins, 70: 1505-1517
Optimal Box Size 1.1:
Manual: http://www.brylinski.org/eboxsize
Original Publication: Feinstein, W. P., Brylinski, M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminf, 7: 18
PyMOL:
Manual: http://pymol.sourceforge.net/newman/userman.pdf
Original Publication: DeLano, W. L. (2002) The PyMOL Molecular Graphics System.
All the programs included in AMDock are open source and freely available to the public
In any case, we have tried hard to be as clear and concise as possible. Comments and questions are welcome, please send them to: