BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

197 related articles for article (PubMed ID: 35759413)

  • 1. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.
    Votapka LW; Stokely AM; Ojha AA; Amaro RE
    J Chem Inf Model; 2022 Jul; 62(13):3253-3262. PubMed ID: 35759413
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach.
    Ahn SH; Jagger BR; Amaro RE
    J Chem Inf Model; 2020 Nov; 60(11):5340-5352. PubMed ID: 32315175
    [TBL] [Abstract][Full Text] [Related]  

  • 3. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.
    Votapka LW; Jagger BR; Heyneman AL; Amaro RE
    J Phys Chem B; 2017 Apr; 121(15):3597-3606. PubMed ID: 28191969
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.
    Jagger BR; Lee CT; Amaro RE
    J Phys Chem Lett; 2018 Sep; 9(17):4941-4948. PubMed ID: 30070844
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach.
    Jagger BR; Ojha AA; Amaro RE
    J Chem Theory Comput; 2020 Aug; 16(8):5348-5357. PubMed ID: 32579371
    [TBL] [Abstract][Full Text] [Related]  

  • 6. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.
    Ojha AA; Votapka LW; Amaro RE
    Chem Sci; 2023 Nov; 14(45):13159-13175. PubMed ID: 38023523
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
    Harger M; Li D; Wang Z; Dalby K; Lagardère L; Piquemal JP; Ponder J; Ren P
    J Comput Chem; 2017 Sep; 38(23):2047-2055. PubMed ID: 28600826
    [TBL] [Abstract][Full Text] [Related]  

  • 8. ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.
    Cardenas AE; Hunter A; Wang H; Elber R
    J Chem Theory Comput; 2022 Nov; 18(11):6952-6965. PubMed ID: 36191005
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.
    Votapka LW; Amaro RE
    PLoS Comput Biol; 2015 Oct; 11(10):e1004381. PubMed ID: 26505480
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes.
    Ruzmetov T; Montes R; Sun J; Chen SH; Tang Z; Chang CA
    J Phys Chem A; 2022 Nov; 126(46):8761-8770. PubMed ID: 36346951
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy.
    Ding Y; Huang J
    Int J Mol Sci; 2024 Jan; 25(3):. PubMed ID: 38338727
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket.
    Wang J; Miao Y
    J Chem Theory Comput; 2023 Feb; 19(3):733-745. PubMed ID: 36706316
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and Compound Design.
    Tang Z; Chen SH; Chang CA
    J Chem Theory Comput; 2020 Mar; 16(3):1882-1895. PubMed ID: 32031801
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Gaussian Accelerated Molecular Dynamics in OpenMM.
    Copeland MM; Do HN; Votapka L; Joshi K; Wang J; Amaro RE; Miao Y
    J Phys Chem B; 2022 Aug; 126(31):5810-5820. PubMed ID: 35895977
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations.
    Sadiq SK; Muñiz Chicharro A; Friedrich P; Wade RC
    J Chem Theory Comput; 2021 Dec; 17(12):7912-7929. PubMed ID: 34739248
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics.
    Huang YM; Kang M; Chang CE
    J Mol Recognit; 2014 Sep; 27(9):537-48. PubMed ID: 25042708
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Advances in computational methods for ligand binding kinetics.
    Sohraby F; Nunes-Alves A
    Trends Biochem Sci; 2023 May; 48(5):437-449. PubMed ID: 36566088
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Milestoning with transition memory.
    Hawk AT; Makarov DE
    J Chem Phys; 2011 Dec; 135(22):224109. PubMed ID: 22168682
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.
    Hopkins CW; Le Grand S; Walker RC; Roitberg AE
    J Chem Theory Comput; 2015 Apr; 11(4):1864-74. PubMed ID: 26574392
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.
    Chiu SH; Xie L
    J Chem Inf Model; 2016 Jun; 56(6):1164-74. PubMed ID: 27159844
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.