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https://github.com/dwhswenson/contact_map

Contact map analysis for biomolecules; based on MDTraj
https://github.com/dwhswenson/contact_map

biochemistry bioinformatics computational-biology molecular-dynamics protein-ligand-interactions protein-protein-interaction

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Contact map analysis for biomolecules; based on MDTraj

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README 

        
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# Contact Map Explorer



This package provides tools for analyzing and exploring contacts

(residue-residue and atom-atom) from a trajectory generated by molecular

dynamics. It builds on the excellent tools provided by

[MDTraj](http://mdtraj.org).



Contacts can be an important tool for defining (meta)stable states in

processes involving biomolecules. For example, an analysis of contacts can

be particularly useful when defining bound states during a binding processes

between proteins, DNA, and small molecules (such as potential drugs).



The contacts analyzed by Contact Map Explorer can be either intermolecular or

intramolecular, and can be analyzed on a residue-residue basis or an atom-atom

basis.



This package makes it very easy to answer questions like:



* What contacts are present in a trajectory?

* Which contacts are most common in a trajectory?

* What is the difference between the frequency of contacts in one trajectory

  and another?  (Or with a specific frame, such as a PDB entry.)

* For a particular residue-residue contact pair of interest, which atoms are

  most frequently in contact?



It also facilitates visualization of the contact matrix, with colors

representing the fraction of trajectory time that the contact was present.



Full documentation is at http://contact-map.readthedocs.io/.



Try it out online: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dwhswenson/contact_map/master?filepath=%2Fexamples) (Note: the performance of the online servers can vary widely.)



## Installation



The easiest way to install is with `conda`. Conda is a powerful package and

environment management system. If you do not already have a highly

customized Python environment, we recommend starting by installing `conda`,

either in the [full anaconda

distribution](https://www.anaconda.com/download/) or the [smaller-footprint

miniconda](https://conda.io/miniconda.html). This package is distributed

through the [conda-forge](http://conda-forge.org) channel; install it with:



```bash

conda install -c conda-forge contact_map

```



If you don't want to use `conda`, you can also use `pip` (via a more

complicated process) or do a developer install. See the [installation

documentation](http://contact-map.readthedocs.io/en/latest/installing.html)

for details.



## Support and development



Contact Map Explorer is an open source project, released under the GNU LGPL,

version 2.1 or (at your option) any later version. Development takes place

in public at https://github.com/dwhswenson/contact_map; your contributions

would be welcome!



If you have suggestions or bug reports, please [raise an issue on our GitHub

issue page](https://github.com/dwhswenson/contact_map/issues).