BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

262 related articles for article (PubMed ID: 30084252)

  • 1. Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions.
    Mishra SK; Koča J
    J Phys Chem B; 2018 Aug; 122(34):8113-8121. PubMed ID: 30084252
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).
    Su PC; Tsai CC; Mehboob S; Hevener KE; Johnson ME
    J Comput Chem; 2015 Sep; 36(25):1859-73. PubMed ID: 26216222
    [TBL] [Abstract][Full Text] [Related]  

  • 3. A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation.
    Chen J; Wang J; Zhang Q; Chen K; Zhu W
    J Biomol Struct Dyn; 2015; 33(12):2606-18. PubMed ID: 25562613
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations.
    Hou T; Wang J; Li Y; Wang W
    J Chem Inf Model; 2011 Jan; 51(1):69-82. PubMed ID: 21117705
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking.
    Chen F; Liu H; Sun H; Pan P; Li Y; Li D; Hou T
    Phys Chem Chem Phys; 2016 Aug; 18(32):22129-39. PubMed ID: 27444142
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.
    Sun H; Duan L; Chen F; Liu H; Wang Z; Pan P; Zhu F; Zhang JZH; Hou T
    Phys Chem Chem Phys; 2018 May; 20(21):14450-14460. PubMed ID: 29785435
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models.
    Mishra SK; Sund J; Åqvist J; Koča J
    J Comput Chem; 2012 Nov; 33(29):2340-50. PubMed ID: 22847637
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein-peptide complexes.
    Weng G; Wang E; Chen F; Sun H; Wang Z; Hou T
    Phys Chem Chem Phys; 2019 May; 21(19):10135-10145. PubMed ID: 31062799
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Develop and test a solvent accessible surface area-based model in conformational entropy calculations.
    Wang J; Hou T
    J Chem Inf Model; 2012 May; 52(5):1199-212. PubMed ID: 22497310
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes.
    Jiang D; Du H; Zhao H; Deng Y; Wu Z; Wang J; Zeng Y; Zhang H; Wang X; Wang E; Hou T; Hsieh CY
    Phys Chem Chem Phys; 2024 Mar; 26(13):10323-10335. PubMed ID: 38501198
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study.
    Ibrahim MA
    J Chem Inf Model; 2011 Oct; 51(10):2549-59. PubMed ID: 21942911
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models.
    Xu L; Sun H; Li Y; Wang J; Hou T
    J Phys Chem B; 2013 Jul; 117(28):8408-21. PubMed ID: 23789789
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches.
    Srivastava HK; Sastry GN
    J Chem Inf Model; 2012 Nov; 52(11):3088-98. PubMed ID: 23121465
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions.
    Wang E; Weng G; Sun H; Du H; Zhu F; Chen F; Wang Z; Hou T
    Phys Chem Chem Phys; 2019 Sep; 21(35):18958-18969. PubMed ID: 31453590
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain.
    Anisimov VM; Cavasotto CN
    J Comput Chem; 2011 Jul; 32(10):2254-63. PubMed ID: 21484840
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking.
    Hou T; Wang J; Li Y; Wang W
    J Comput Chem; 2011 Apr; 32(5):866-77. PubMed ID: 20949517
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.
    Wang B; Li L; Hurley TD; Meroueh SO
    J Chem Inf Model; 2013 Oct; 53(10):2659-70. PubMed ID: 24032517
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Affinity Calculations of Cyclodextrin Host-Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods.
    Suárez D; Díaz N
    J Chem Inf Model; 2019 Jan; 59(1):421-440. PubMed ID: 30566348
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.
    Ferrari AM; Degliesposti G; Sgobba M; Rastelli G
    Bioorg Med Chem; 2007 Dec; 15(24):7865-77. PubMed ID: 17870536
    [TBL] [Abstract][Full Text] [Related]  

  • 20. A QM/MM study of the binding of RAPTA ligands to cathepsin B.
    Ciancetta A; Genheden S; Ryde U
    J Comput Aided Mol Des; 2011 Aug; 25(8):729-42. PubMed ID: 21701919
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 14.