Use organic solvents in your Drug Design project

With pyMDMix python package, easily set up and analyze molecular dynamics simulations of your target protein to unveil high affinity interaction spots and characterize their chemical nature.

Welcome to MDMix website

MDMix methodology, applied in the field of computational drug discovery, identifies high affinity interaction spots over macromolecular systems by means of molecular dynamics simulations using solvent mixtures as solvation conditions. pyMDMix is a python module and user interface that aims to ease the application of such technique.

In this site you will learn about the MDMix methodology and how it can be useful in your Structure Based Drug Design project (SBDD). Learn to install and use pyMDMix package here presented to set up and analyze simulations of the biomolecule target of your project in aqueous-organic mixtures.

Head to MDMis method for discovering the applications and motivations behind the project or jump to pyMDMix sections where you can find documentation about the program.

Recent blog posts

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Solving Installation issues (the Biskit oldnumeric problem)

As some users have noticed, newer versions of numpy are incompatible with one of the main dependencies for pyMDmix installation: Biskit. Biskit uses an older version of numpy (Numeric, or oldnumeric in the code) that is currently obsolete and not supported anymore. Because of that, installation of pyMDmix fails! But don´t worry, I solved the […]

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Tutorial 1a: Preparing a toy project

To follow this tutorial a basic knowledge on linux is needed (create, move, copy, edit files and directories). 1) Prepare a PDB file with your system to simulate Download the following PDB file with a toy 8 aminoacid peptide PDB (pep.pdb). The molecule was built using MOE software, protonated and saved following AMBER naming convention. […]

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Tutorial 1b: Simulating the toy project

1) The COMMANDS.sh file We have our project folder pep_amber created in Tutorial 1a ready for simulation. It contains 2 folders inside MD directory: ETA_1 and WAT_1. Each one contains all files needed to run an independent simulation: system topology, coordinates, min/ eq/ and md/ folders with the configuration files for each simulation step and, […]

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Tutorial 1c: Analyzing the toy project

0) Download the finished toy project If you didn’t follow all the setup and simulation run, you can download the completed toy project started in Tutorial 1a with the simulation results from here. Extract the folder to proceed and move to the project directory (pep_amber) to start with the analysis. 1) Check project status Execute […]

Get it!

Download source files and follow online documentation for installation instructions

Get pyMDMix

Installation Guide

pyMDMix is easily installed in any platform. It is tested under Linux and Mac OSX platforms. Follow this link to check installation instructions.

Installation

Tutorials

Find starting tutorials in the Blog. More tutorials on detailed topics will be uploaded soon.

Tutorial