index.rst

MSMBuilder

Statistical models for Biomolecular Dynamics

MSMBuilder is an application and python library. It builds statistical models for high-dimensional time-series. The particular focus of the package is on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change.

To get started via Anaconda Python, use:

conda install -c omnia msmbuilder

MSMBuilder includes algorithms for constructing dynamical models:

• :ref:`featurization`
• :ref:`feature_selection`
• :ref:`preprocessing`
• :ref:`decomposition`
• :ref:`cluster`
• :ref:`msm`
• :ref:`hmm`
• :ref:`ratematrix`

As well as methods for analysis and validation of the models:

• :ref:`gmrq`
• :ref:`tpt`

New users should check out:

• :ref:`background`
• :ref:`installation`
• :ref:`tutorial`
• :ref:`examples`
• :ref:`faq`

MSMBuilder is most effective as a library. Intermediate users should familiarize themselves with:

• :ref:`apipatterns`
• :ref:`datasets`
• :ref:`changelog`

MSMBuilder is developed by primarily by researchers at Stanford University, and we welcome contributions. The development all takes place on Github. MSMBuilder is licensed under the GNU LGPL (v2.1 or later).

.. toctree::
    :maxdepth: 2
    :hidden:

    background
    installation
    tutorial
    examples/index
    featurization
    feature_selection
    preprocessing
    decomposition
    cluster
    msm
    gmrq
    tpt
    ratematrix
    hmm
    datasets
    io
    apipatterns
    plugins
    faq
    changelog
    publications
    contributing