BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

320 related articles for article (PubMed ID: 28024402)

  • 1. 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]  

  • 2. 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]  

  • 3. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.
    Athanasiou C; Vasilakaki S; Dellis D; Cournia Z
    J Comput Aided Mol Des; 2018 Jan; 32(1):21-44. PubMed ID: 29119352
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 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. 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]  

  • 8. 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]  

  • 9. 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]  

  • 10. Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics.
    Raman EP; Paul TJ; Hayes RL; Brooks CL
    J Chem Theory Comput; 2020 Dec; 16(12):7895-7914. PubMed ID: 33201701
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Towards predictive ligand design with free-energy based computational methods?
    Foloppe N; Hubbard R
    Curr Med Chem; 2006; 13(29):3583-608. PubMed ID: 17168725
    [TBL] [Abstract][Full Text] [Related]  

  • 12. 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]  

  • 13. Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures.
    Beuming T; Martín H; Díaz-Rovira AM; Díaz L; Guallar V; Ray SS
    J Chem Inf Model; 2022 Sep; 62(18):4351-4360. PubMed ID: 36099477
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Accurate Binding Free Energy Predictions in Fragment Optimization.
    Steinbrecher TB; Dahlgren M; Cappel D; Lin T; Wang L; Krilov G; Abel R; Friesner R; Sherman W
    J Chem Inf Model; 2015 Nov; 55(11):2411-20. PubMed ID: 26457994
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Predicting Activity Cliffs with Free-Energy Perturbation.
    Pérez-Benito L; Casajuana-Martin N; Jiménez-Rosés M; van Vlijmen H; Tresadern G
    J Chem Theory Comput; 2019 Mar; 15(3):1884-1895. PubMed ID: 30776226
    [TBL] [Abstract][Full Text] [Related]  

  • 16. 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]  

  • 17. 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]  

  • 18. 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]  

  • 19. 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]  

  • 20. Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models.
    Xu T; Zhu K; Beautrait A; Vendome J; Borrelli KW; Abel R; Friesner RA; Miller EB
    J Chem Theory Comput; 2022 Sep; 18(9):5710-5724. PubMed ID: 35972903
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 16.