madamm
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madamm [2013/10/02 15:47] nuno |
madamm [2013/10/03 09:56] (current) nuno [2. ScreenShots] |
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| //Operating systems: MacOS and Linux.// | //Operating systems: MacOS and Linux.// | ||
| - | {{:b-download.png?direct&100|}} | + | [[http://www.fc.up.pt/pessoas/nscerque/download/MADAMM.tar.gz|{{:b-download.png?direct&100|}}]] |
| Contacts : [[nscerque@fc.up.pt|Nuno Sousa Cerqueira]] [[pafernan@fc.up.pt|Pedro A. Fernandes]] [[mjramos@fc.up.pt|Maria João Ramos]] | Contacts : [[nscerque@fc.up.pt|Nuno Sousa Cerqueira]] [[pafernan@fc.up.pt|Pedro A. Fernandes]] [[mjramos@fc.up.pt|Maria João Ramos]] | ||
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| <WRAP column 15%> | <WRAP column 15%> | ||
| - | {{:quantumchemcirty.gif?direct&100|}} | + | {{:madammcover.gif?direct&200|}} |
| </WRAP> | </WRAP> | ||
| - | **__Citation :__** \\ | + | **__Citation :__** |
| + | |||
| + | //MADAMM: a multistaged docking with an automated molecular modeling protocol.//\\ | ||
| + | N. M. F. S. A. Cerqueira, N. F. Bras, P. A. Fernandes AND M. J. Ramos\\ | ||
| + | Proteins (Structure, Function, Bioinformatics), 2009, 74(1):192–206 | ||
| + | [[http://onlinelibrary.wiley.com/doi/10.1002/prot.22146/full|DOI:10.1002/prot.22146]] | ||
| - | //VsLab—An implementation for virtual high-throughput screening using AutoDock and VMD.//\\ | ||
| - | N. M. F. S. A. Cerqueira, J. Ribeiro, P. A. Fernandes AND M. J. Ramos \\ | ||
| - | International Journal of Quantum Chemistry, 2011, 111(6):1208–1212 | ||
| - | [[http://onlinelibrary.wiley.com/doi/10.1002/qua.22738/full|DOI:10.1002/qua.22738]]\\ | ||
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| ===== 1. Introduction ===== | ===== 1. Introduction ===== | ||
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| <note tip> | <note tip> | ||
| - | * MADAMM : **v1.0** {{:b-download.png?direct&100|}} | + | * MADAMM : **v1.0** [[http://www.fc.up.pt/pessoas/nscerque/download/MADAMM.tar.gz|{{:b-download.png?direct&100|}}]] |
| </note> | </note> | ||
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| ===== 4. Installation ===== | ===== 4. Installation ===== | ||
| ### | ### | ||
| - | VsLab can only be installed in LINUX and MAC operating systems, due to the limitations of the GOLD and Charmm software. | + | MADAMM can only be installed in LINUX and MAC operating systems, due to the limitations of the GOLD and Charmm software. |
| ### | ### | ||
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| ### | ### | ||
| - | * tcl/tk | + | * **tcl/tk** |
| ### | ### | ||
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| tar -xvzf ActiveTcl8.4.14.0.272572-linux-ix86.tar.gz | tar -xvzf ActiveTcl8.4.14.0.272572-linux-ix86.tar.gz | ||
| cd ActiveTcl8.4.14.0.272572-linux-ix86/ | cd ActiveTcl8.4.14.0.272572-linux-ix86/ | ||
| - | ./install.sh (note : you must have root permissions for this command) | + | ./install.sh (note : you must have root permissions for this command) |
| - | *VMD | + | * **VMD** |
| ### | ### | ||
| MADAMM has a small interface that allows to analyse all the results using VMD. | MADAMM has a small interface that allows to analyse all the results using VMD. | ||
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| ### | ### | ||
| - | *gnuPLOT | + | * **gnuPLOT** |
| ### | ### | ||
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| ### | ### | ||
| - | *GOLD and CHARMm | + | * **GOLD and CHARMm** |
| ### | ### | ||
| You need these proprietary software to run the docking software and the molecular mechanics forcefield that are the required by MADAMM. | You need these proprietary software to run the docking software and the molecular mechanics forcefield that are the required by MADAMM. | ||
madamm.1380725268.txt.gz · Last modified: 2013/10/02 15:47 by nuno
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