compasm
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compasm [2013/10/02 16:33] nuno |
compasm [2013/10/03 09:53] (current) nuno [2. ScreenShots] |
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| {{:b-download.png?direct&100|}} [[vmdmagazinedatabase|{{:b-database.png?direct&100|}}]] | {{:b-download.png?direct&100|}} [[vmdmagazinedatabase|{{:b-database.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 : [[jrvribeiro@gmail.com|João Ribeiro]] [[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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| //CompASM: an Amber-VMD alanine scanning mutagenesis plug-in.//\\ | //CompASM: an Amber-VMD alanine scanning mutagenesis plug-in.//\\ | ||
| J. Ribeiro, N. M. F. S. A. Cerqueira, I. S. Moreira, P. A. Fernandes AND M. J. Ramos \\ | J. Ribeiro, N. M. F. S. A. Cerqueira, I. S. Moreira, P. A. Fernandes AND M. J. Ramos \\ | ||
| - | Theoretical Chemistry Accounts, 2012, 131:1271 | + | Theoretical Chemistry Accounts, 2012, 131:1271\\ |
| [[http://link.springer.com/article/10.1007%2Fs00214-012-1271-2|10.1007/s00214-012-1271-2]]\\ | [[http://link.springer.com/article/10.1007%2Fs00214-012-1271-2|10.1007/s00214-012-1271-2]]\\ | ||
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| ===== 1. Introduction ===== | ===== 1. Introduction ===== | ||
| ### | ### | ||
| + | Protein-protein interactions play a crucial role in molecular recognition and cellular function. Mapping them, provides important insight on how these structures interact and on how to improve or inhibit their binding. | ||
| + | ### | ||
| + | ### | ||
| + | CompASM presents here as a very intuitive plug-in for two widely distributed softwares ( AMBER-Visual Molecular Dynamics (VMD)) that allows the user to perform a full Alanine Scanning Mutagenesis (ASM) procedure, requiring only very little user effort. This software is composed by two main packages: the Core and Graphical User Interface (GUI). | ||
| + | ### | ||
| + | ### | ||
| + | The CompASM Core section (Amber dependent, VMD independent) contains the main procedures of the ASM algorithm, e.g. Molecular Dynamics Simulation and MMPBSA calculation. It can be launched in a shell command and/or with the “Run” button of the GUI. | ||
| + | ### | ||
| + | ### | ||
| + | The CompASM GUI section (Amber independent, VMD dependent) turns possible the communication between Amber and VMD. Here, the user can generate the input file and submit it to the CompASM Core automatically, as well as being able to visualize the interfaces and the final results. | ||
| ### | ### | ||
| ===== 2. ScreenShots ===== | ===== 2. ScreenShots ===== | ||
| - | {{gallery>software:compasm:screenshots?*&150x150&lightbox}} | + | {{gallery>software::compasm?*&150x150&lightbox}} |
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| - Install the VMD software ( if you haven't yet installed). | - Install the VMD software ( if you haven't yet installed). | ||
| - | - Extract vmdMagazine.zip file to a directory in the disk. | + | - Download the CompASM package. |
| - | - Once unpacked, we need to let VMD know of this location. To do so, edit your VMD start-up file and add the biopathfinder plugin directory to the auto_path variable (see below). | + | - Uncompress the tar.gz (or .zip) file to your Desktop folder |
| - | - Once this procedure is complete the BioPathFinder plugin can be found at the VMD extensions menu (CompBioComp>>vmdMagazine). | + | - Run the installation program: |
| - | | + | |
| + | |||
| + | Unix OS- Open a shell window and type: | ||
| + | cd | ||
| + | cd Desktop/CompASM | ||
| + | tclsh8.5 install.tcl | ||
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| + | |||
| + | Windows- Double-click on the install.tcl file | ||
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| + | |||
| + | - Follow the instructions given in the window | ||
| + | - Start VMD. | ||
| + | - Edit amber_run.sh file to a proper sander launch (file containing the command to launch sander tool) | ||
compasm.1380728013.txt.gz · Last modified: 2013/10/02 16:33 by nuno
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