Is there anyone who can tell me how can you predict a molecular interaction between two factors or proteins , using bioinformatic analysis ? what kind of software or website can i use ?
I have been using Gromacs for studying molecular interactions and simulations. Hope this works for your question.
More information are needed. And if you have never run MD simulation before, you should go through the tutorials at http://www.gromacs.org/Documentation/Tutorials. It's a long way to learn MD simulation by yourself. It's more like a Mission Impossible.
For Gromacs, You need to have Linux platform and the installation is directed using Terminal of Linux.
SDA 6.0 is another software for Molecular Dynamics which again needs Linux platform.
http://www.gromacs.org/Documentation/Installation_Instructions
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