Seekrtools: Multiscale Milestoning Calculations of Kinetics Tools
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:Release: |release|
:Date: |today|

**Seekrtools** Simulation Enabled Estimation of Kinetic Rates Tools
is a set of software tools that interfaces with SEEKR programs, 
most notably with SEEKR2, in order to prepare and facilitate multiscale
milestoning calculations.

Seekrtools provides content that can facilitate a number of tasks for SEEKR2
users, including:

 1. Documentation, sample scripts, and tutorials to help users prepare systems
    for SEEKR2 calculations, including

  * a. parametrization
  * b. minimization/equilibration
  * c. steered molecular dynamics (SMD) and other methods to generate starting structures
   
 2. More tools for analysis of SEEKR2 results.
 3. Additional example systems and SEEKR2 inputs to explore and test SEEKR2 
    features
   
  * New/experimental collective variables (CVs)
  * Unusual systems with multiple sites/important motions
  * New applications of milestoning theory

.. toctree::
   :maxdepth: 1
   :caption: Contents:

   installation
   tutorial
   program_options

Cite SEEKR2
===========

If you use SeekrTools, please cite the following paper:

* Votapka, L. W.; Stokely, A. M.; Ojha, A. A.; Amaro, R. E. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J. Chem. Inf. Mod. 2022 62 (13), 3253-3262. DOI: 10.1021/acs.jcim.2c00501

You may also optionally cite one or more of the following papers:

* Votapka, L. W.; Jagger, B. R.; Heyneman, A. L.; Amaro, R. E. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding. J. Phys. Chem. B 2017, 121 (15), 3597–3606. https://doi.org/10.1021/acs.jpcb.6b09388. 

* Jagger, B. R.; Ojha, A. A.; Amaro, R. E. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. J. Chem. Theory Comput. 2020. https://doi.org/10.1021/acs.jctc.0c00495. 

* Jagger, B. R.; Lee, C. T.; Amaro, R. E. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J. Phys. Chem. Lett. 2018, 9 (17), 4941–4948. https://doi.org/10.1021/acs.jpclett.8b02047. 

* Votapka LW, Amaro RE (2015) Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLOS Computational Biology 11(10): e1004381. https://doi.org/10.1371/journal.pcbi.1004381


Getting Involved
================

Please report **bugs** or **enhancement requests** through the `Issue 
Tracker`_. 

.. _Issue Tracker: https://github.com/seekrcentral/seekrtools/issues

Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`