SEEKR

SEEKR is a software tool to compute multiscale molecular binding, unbinding, and transport kinetics. The SEEKR algorithm uses molecular dynamics, Brownian dynamics, and milestoning theory.

Topic

Protein binding sites;Protein interactions;Proteins;Simulation experiment

Detail

  • Operation: Enzyme kinetics calculation

  • Software interface: Command-line user interface

  • Language: -

  • License: The MIT License

  • Cost: Free

  • Version name: 2

  • Credit: The National Science Foundation Graduate Research Fellowship Program, the NIH Molecular Biophysics Training Program, the NIH Directors New Innovator Award, the National Biomedical Computation Resource (NBCR) NIH.

  • Input: -

  • Output: -

  • Contact: Rommie E Amaro ramaro@ucsd.edu

  • Collection: -

  • Maturity: Stable

Publications

  • SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine
  • Votapka LW, Stokely AM, Ojha AA, Amaro RE. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J Chem Inf Model. 2022 Jun 27. doi: 10.1021/acs.jcim.2c00501. Epub ahead of print. PMID: 35759413.
  • https://doi.org/10.1021/acs.jcim.2c00501
  • PMID: 35759413
  • PMC: -
  • Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach
  • Jagger BR, Ojha AA, Amaro RE. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. J Chem Theory Comput. 2020 Aug 11;16(8):5348-5357. doi: 10.1021/acs.jctc.0c00495. Epub 2020 Jul 9. PMID: 32579371.
  • https://doi.org/10.1021/acs.jctc.0c00495
  • PMID: 32579371
  • PMC: -
  • SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
  • Votapka LW, et al. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. 2017; 121:3597-3606. doi: 10.1021/acs.jpcb.6b09388
  • https://doi.org/10.1021/acs.jpcb.6b09388
  • PMID: 28191969
  • PMC: PMC5562489
  • Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach
  • Jagger BR, Lee CT, Amaro RE. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. J Phys Chem Lett. 2018 Sep 6;9(17):4941-4948. doi: 10.1021/acs.jpclett.8b02047. Epub 2018 Aug 16. PMID: 30070844; PMCID: PMC6443090.
  • https://doi.org/10.1021/acs.jpclett.8b02047
  • PMID: 30070844
  • PMC: PMC6443090
  • Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
  • Votapka LW, Amaro RE. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol. 2015 Oct 27;11(10):e1004381. doi: 10.1371/journal.pcbi.1004381. PMID: 26505480; PMCID: PMC4624728.
  • https://doi.org/10.1371/journal.pcbi.1004381
  • PMID: 26505480
  • PMC: PMC4624728

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