BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

387 related articles for article (PubMed ID: 36282990)

  • 1. Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling.
    Liu W; Liu Z; Liu H; Westerhoff LM; Zheng Z
    J Chem Inf Model; 2022 Nov; 62(22):5645-5665. PubMed ID: 36282990
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study.
    Xue S; Liu H; Zheng Z
    Int J Mol Sci; 2019 Sep; 20(19):. PubMed ID: 31569580
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Integrating Molecular Docking and Molecular Dynamics Simulations.
    Santos LHS; Ferreira RS; Caffarena ER
    Methods Mol Biol; 2019; 2053():13-34. PubMed ID: 31452096
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Molecular Dynamics as a Tool for Virtual Ligand Screening.
    Menchon G; Maveyraud L; Czaplicki G
    Methods Mol Biol; 2018; 1762():145-178. PubMed ID: 29594772
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Rescoring of docking poses under Occam's Razor: are there simpler solutions?
    Zhenin M; Bahia MS; Marcou G; Varnek A; Senderowitz H; Horvath D
    J Comput Aided Mol Des; 2018 Sep; 32(9):877-888. PubMed ID: 30173397
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
    Gill SC; Lim NM; Grinaway PB; Rustenburg AS; Fass J; Ross GA; Chodera JD; Mobley DL
    J Phys Chem B; 2018 May; 122(21):5579-5598. PubMed ID: 29486559
    [TBL] [Abstract][Full Text] [Related]  

  • 7. On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.
    Bansal N; Zheng Z; Cerutti DS; Merz KM
    J Comput Aided Mol Des; 2017 Jan; 31(1):47-60. PubMed ID: 27699553
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Advances in Docking.
    Sulimov VB; Kutov DC; Sulimov AV
    Curr Med Chem; 2019; 26(42):7555-7580. PubMed ID: 30182836
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015.
    Deng N; Flynn WF; Xia J; Vijayan RS; Zhang B; He P; Mentes A; Gallicchio E; Levy RM
    J Comput Aided Mol Des; 2016 Sep; 30(9):743-751. PubMed ID: 27562018
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study.
    Liu K; Kokubo H
    J Chem Inf Model; 2017 Oct; 57(10):2514-2522. PubMed ID: 28902511
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Receptor-Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method.
    Liu H; Deng J; Luo Z; Lin Y; Merz KM; Zheng Z
    J Chem Theory Comput; 2020 Oct; 16(10):6645-6655. PubMed ID: 32857938
    [TBL] [Abstract][Full Text] [Related]  

  • 12. CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.
    Guterres H; Im W
    J Chem Inf Model; 2023 Aug; 63(15):4772-4779. PubMed ID: 37462607
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.
    Wu Y; Brooks CL
    J Chem Inf Model; 2021 Nov; 61(11):5535-5549. PubMed ID: 34704754
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Molecular Dynamics as a Tool for Virtual Ligand Screening.
    Menchon G; Maveyraud L; Czaplicki G
    Methods Mol Biol; 2024; 2714():33-83. PubMed ID: 37676592
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations.
    Shen M; Zhou S; Li Y; Pan P; Zhang L; Hou T
    Mol Biosyst; 2013 Mar; 9(3):361-74. PubMed ID: 23340525
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Relative Binding Free Energy Calculations Applied to Protein Homology Models.
    Cappel D; Hall ML; Lenselink EB; Beuming T; Qi J; Bradner J; Sherman W
    J Chem Inf Model; 2016 Dec; 56(12):2388-2400. PubMed ID: 28024402
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
    Cournia Z; Allen B; Sherman W
    J Chem Inf Model; 2017 Dec; 57(12):2911-2937. PubMed ID: 29243483
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.
    Greenidge PA; Kramer C; Mozziconacci JC; Sherman W
    J Chem Inf Model; 2014 Oct; 54(10):2697-717. PubMed ID: 25266271
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations.
    Ben-Shalom IY; Pfeiffer-Marek S; Baringhaus KH; Gohlke H
    J Chem Inf Model; 2017 Feb; 57(2):170-189. PubMed ID: 27996253
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships.
    Naqvi AAT; Mohammad T; Hasan GM; Hassan MI
    Curr Top Med Chem; 2018; 18(20):1755-1768. PubMed ID: 30360721
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 20.