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 *

813 related articles for article (PubMed ID: 31396905)

  • 1. 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]  

  • 2. 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]  

  • 3. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery.
    Wang L; Deng Y; Wu Y; Kim B; LeBard DN; Wandschneider D; Beachy M; Friesner RA; Abel R
    J Chem Theory Comput; 2017 Jan; 13(1):42-54. PubMed ID: 27933808
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 6. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches.
    Raman EP; Lakkaraju SK; Denny RA; MacKerell AD
    J Comput Chem; 2017 Jun; 38(15):1238-1251. PubMed ID: 27782307
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites?
    Lockhart C; Luo X; Olson A; Delfing BM; Laracuente XE; Foreman KW; Paige M; Kehn-Hall K; Klimov DK
    J Chem Inf Model; 2023 Aug; 63(15):4791-4802. PubMed ID: 37531558
    [TBL] [Abstract][Full Text] [Related]  

  • 8. A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.
    Abel R; Wang L; Mobley DL; Friesner RA
    Curr Top Med Chem; 2017; 17(23):2577-2585. PubMed ID: 28413950
    [TBL] [Abstract][Full Text] [Related]  

  • 9. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
    Kaus JW; Harder E; Lin T; Abel R; McCammon JA; Wang L
    J Chem Theory Comput; 2015 Jun; 11(6):2670-9. PubMed ID: 26085821
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?
    Procacci P
    Molecules; 2022 Jul; 27(14):. PubMed ID: 35889299
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Exploring the Effectiveness of Binding Free Energy Calculations.
    Mondal D; Florian J; Warshel A
    J Phys Chem B; 2019 Oct; 123(42):8910-8915. PubMed ID: 31560539
    [TBL] [Abstract][Full Text] [Related]  

  • 12. 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]  

  • 13. Absolute Binding Free Energy Calculation and Design of a Subnanomolar Inhibitor of Phosphodiesterase-10.
    Li Z; Huang Y; Wu Y; Chen J; Wu D; Zhan CG; Luo HB
    J Med Chem; 2019 Feb; 62(4):2099-2111. PubMed ID: 30689375
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols.
    Bhati AP; Coveney PV
    J Chem Theory Comput; 2022 Apr; 18(4):2687-2702. PubMed ID: 35293737
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.
    Jiang W; Thirman J; Jo S; Roux B
    J Phys Chem B; 2018 Oct; 122(41):9435-9442. PubMed ID: 30253098
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3.
    He X; Man VH; Ji B; Xie XQ; Wang J
    J Comput Aided Mol Des; 2019 Jan; 33(1):105-117. PubMed ID: 30218199
    [TBL] [Abstract][Full Text] [Related]  

  • 17. An Improved Free Energy Perturbation FEP+ Sampling Protocol for Flexible Ligand-Binding Domains.
    Fratev F; Sirimulla S
    Sci Rep; 2019 Nov; 9(1):16829. PubMed ID: 31728038
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Free Energy Calculations for Protein-Ligand Binding Prediction.
    Jespers W; Åqvist J; Gutiérrez-de-Terán H
    Methods Mol Biol; 2021; 2266():203-226. PubMed ID: 33759129
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Perspective: Alchemical free energy calculations for drug discovery.
    Mobley DL; Klimovich PV
    J Chem Phys; 2012 Dec; 137(23):230901. PubMed ID: 23267463
    [TBL] [Abstract][Full Text] [Related]  

  • 20. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
    Jo S; Jiang W; Lee HS; Roux B; Im W
    J Chem Inf Model; 2013 Jan; 53(1):267-77. PubMed ID: 23205773
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 41.