Seekrtools: Multiscale Milestoning Calculations of Kinetics Tools

Release:

Date:

May 04, 2026

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

    1. parametrization

    1. minimization/equilibration

    1. steered molecular dynamics (SMD) and other methods to generate starting structures

  1. More tools for analysis of SEEKR2 results.

  2. 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

Contents:

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.

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