These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

184 related articles for article (PubMed ID: 31743019)

  • 1. Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix.
    Cui D; Zhang BW; Tan Z; Levy RM
    J Chem Theory Comput; 2020 Jan; 16(1):67-79. PubMed ID: 31743019
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.
    Kim I; Allen TW
    J Chem Phys; 2012 Apr; 136(16):164103. PubMed ID: 22559466
    [TBL] [Abstract][Full Text] [Related]  

  • 3. The UWHAM and SWHAM Software Package.
    Zhang BW; Arasteh S; Levy RM
    Sci Rep; 2019 Feb; 9(1):2803. PubMed ID: 30808938
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Classical and Machine Learning Methods for Protein - Ligand Binding Free Energy Estimation.
    Sivakumar D; Wu S
    Curr Drug Metab; 2022; 23(4):252-259. PubMed ID: 35293293
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A Stochastic Solution to the Unbinned WHAM Equations.
    Zhang BW; Xia J; Tan Z; Levy RM
    J Phys Chem Lett; 2015 Oct; 6(19):3834-40. PubMed ID: 26722879
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.
    Ding X; Vilseck JZ; Brooks CL
    J Chem Theory Comput; 2019 Feb; 15(2):799-802. PubMed ID: 30689377
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.
    Shirts MR; Pande VS
    J Chem Phys; 2005 Apr; 122(14):144107. PubMed ID: 15847516
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules.
    Wahl J; Smieško M
    J Chem Inf Model; 2019 Feb; 59(2):754-765. PubMed ID: 30640456
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium.
    Zhang BW; Deng N; Tan Z; Levy RM
    J Chem Theory Comput; 2017 Oct; 13(10):4660-4674. PubMed ID: 28902500
    [TBL] [Abstract][Full Text] [Related]  

  • 10. An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations.
    Li Y; Liu R; Liu J; Luo H; Wu C; Li Z
    J Chem Inf Model; 2023 Jan; 63(2):561-570. PubMed ID: 36583975
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY; Chu ZT; Tao H; Warshel A
    Proteins; 2000 Jun; 39(4):393-407. PubMed ID: 10813821
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.
    Lu N; Kofke DA; Woolf TB
    J Comput Chem; 2004 Jan; 25(1):28-39. PubMed ID: 14634991
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Protein-Ligand Binding Free Energy Calculations with FEP.
    Wang L; Chambers J; Abel R
    Methods Mol Biol; 2019; 2022():201-232. PubMed ID: 31396905
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Advancing Drug Discovery through Enhanced Free Energy Calculations.
    Abel R; Wang L; Harder ED; Berne BJ; Friesner RA
    Acc Chem Res; 2017 Jul; 50(7):1625-1632. PubMed ID: 28677954
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A New Approach for Estimating the Free Energy Differences among Multiple Thermodynamic States in Statistical Simulations.
    Yang J; Singer SJ
    J Phys Chem Lett; 2023 Jun; 14(22):5127-5133. PubMed ID: 37249593
    [TBL] [Abstract][Full Text] [Related]  

  • 16. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling.
    König G; Glaser N; Schroeder B; Kubincová A; Hünenberger PH; Riniker S
    J Chem Inf Model; 2020 Nov; 60(11):5407-5423. PubMed ID: 32794763
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.
    Wang L; Deng Y; Knight JL; Wu Y; Kim B; Sherman W; Shelley JC; Lin T; Abel R
    J Chem Theory Comput; 2013 Feb; 9(2):1282-93. PubMed ID: 26588769
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.
    Tan Z; Xia J; Zhang BW; Levy RM
    J Chem Phys; 2016 Jan; 144(3):034107. PubMed ID: 26801020
    [TBL] [Abstract][Full Text] [Related]  

  • 19. To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough.
    Pitman M; Hahn DF; Tresadern G; Mobley DL
    J Chem Inf Model; 2023 Mar; 63(6):1776-1793. PubMed ID: 36878475
    [TBL] [Abstract][Full Text] [Related]  

  • 20. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.
    Gapsys V; Seeliger D; de Groot BL
    J Chem Theory Comput; 2012 Jul; 8(7):2373-82. PubMed ID: 26588970
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.