BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

222 related articles for article (PubMed ID: 30689375)

  • 1. 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]  

  • 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. Advances in binding free energies calculations: QM/MM-based free energy perturbation method for drug design.
    Rathore RS; Sumakanth M; Reddy MS; Reddanna P; Rao AA; Erion MD; Reddy MR
    Curr Pharm Des; 2013; 19(26):4674-86. PubMed ID: 23260025
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Application of Free Energy Perturbation (FEP+) to Understanding Ligand Selectivity: A Case Study to Assess Selectivity Between Pairs of Phosphodiesterases (PDE's).
    Moraca F; Negri A; de Oliveira C; Abel R
    J Chem Inf Model; 2019 Jun; 59(6):2729-2740. PubMed ID: 31144815
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. 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]  

  • 7. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.
    Kim S; Oshima H; Zhang H; Kern NR; Re S; Lee J; Roux B; Sugita Y; Jiang W; Im W
    J Chem Theory Comput; 2020 Nov; 16(11):7207-7218. PubMed ID: 33112150
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. Free energy perturbation (FEP)-guided scaffold hopping.
    Wu D; Zheng X; Liu R; Li Z; Jiang Z; Zhou Q; Huang Y; Wu XN; Zhang C; Huang YY; Luo HB
    Acta Pharm Sin B; 2022 Mar; 12(3):1351-1362. PubMed ID: 35530128
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function.
    Liu R; Li W; Yao Y; Wu Y; Luo HB; Li Z
    J Chem Inf Model; 2023 Dec; 63(24):7755-7767. PubMed ID: 38048439
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach.
    Reddy MR; Erion MD
    J Am Chem Soc; 2001 Jul; 123(26):6246-52. PubMed ID: 11427047
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation.
    Liang L; Liu H; Xing G; Deng C; Hua Y; Gu R; Lu T; Chen Y; Zhang Y
    Phys Chem Chem Phys; 2022 May; 24(17):9904-9920. PubMed ID: 35416820
    [TBL] [Abstract][Full Text] [Related]  

  • 14. 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]  

  • 15. 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]  

  • 16. Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease.
    Ghahremanpour MM; Saar A; Tirado-Rives J; Jorgensen WL
    J Chem Inf Model; 2023 Aug; 63(16):5309-5318. PubMed ID: 37561001
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method.
    Oshima H; Re S; Sugita Y
    J Chem Inf Model; 2020 Nov; 60(11):5382-5394. PubMed ID: 32786707
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor.
    Qian Y; Cabeza de Vaca I; Vilseck JZ; Cole DJ; Tirado-Rives J; Jorgensen WL
    J Phys Chem B; 2019 Oct; 123(41):8675-8685. PubMed ID: 31553604
    [TBL] [Abstract][Full Text] [Related]  

  • 19. 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]  

  • 20. New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes.
    Valiente PA; Gil A; Batista PR; Caffarena ER; Pons T; Pascutti PG
    J Comput Chem; 2010 Nov; 31(15):2723-34. PubMed ID: 20839299
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.