BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

173 related articles for article (PubMed ID: 32315175)

  • 1. 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]  

  • 2. 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]  

  • 3. 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]  

  • 4. 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]  

  • 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. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.
    Ray D; Gokey T; Mobley DL; Andricioaei I
    J Chem Phys; 2020 Oct; 153(15):154117. PubMed ID: 33092382
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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]  

  • 8. 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]  

  • 9. 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]  

  • 10. Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.
    Dixon T; Lotz SD; Dickson A
    J Comput Aided Mol Des; 2018 Oct; 32(10):1001-1012. PubMed ID: 30141102
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Markovian Weighted Ensemble Milestoning (M-WEM): Long-Time Kinetics from Short Trajectories.
    Ray D; Stone SE; Andricioaei I
    J Chem Theory Comput; 2022 Jan; 18(1):79-95. PubMed ID: 34910499
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics.
    Badaoui M; Buigues PJ; Berta D; Mandana GM; Gu H; Földes T; Dickson CJ; Hornak V; Kato M; Molteni C; Parsons S; Rosta E
    J Chem Theory Comput; 2022 Apr; 18(4):2543-2555. PubMed ID: 35195418
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. Role of water and steric constraints in the kinetics of cavity-ligand unbinding.
    Tiwary P; Mondal J; Morrone JA; Berne BJ
    Proc Natl Acad Sci U S A; 2015 Sep; 112(39):12015-9. PubMed ID: 26371312
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. How Effectively Can Adaptive Sampling Methods Capture Spontaneous Ligand Binding?
    Betz RM; Dror RO
    J Chem Theory Comput; 2019 Mar; 15(3):2053-2063. PubMed ID: 30645108
    [TBL] [Abstract][Full Text] [Related]  

  • 17. The prediction of protein-ligand unbinding for modern drug discovery.
    Zhang Q; Zhao N; Meng X; Yu F; Yao X; Liu H
    Expert Opin Drug Discov; 2022 Feb; 17(2):191-205. PubMed ID: 34731059
    [TBL] [Abstract][Full Text] [Related]  

  • 18. 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]  

  • 19. Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges.
    Wolf S
    J Chem Inf Model; 2023 May; 63(10):2902-2910. PubMed ID: 37133392
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Investigating Drug-Target Residence Time in Kinases through Enhanced Sampling Simulations.
    Gobbo D; Piretti V; Di Martino RMC; Tripathi SK; Giabbai B; Storici P; Demitri N; Girotto S; Decherchi S; Cavalli A
    J Chem Theory Comput; 2019 Aug; 15(8):4646-4659. PubMed ID: 31246463
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 9.