232 related articles for article (PubMed ID: 29930024)
1. Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.
Chen F; Sun H; Wang J; Zhu F; Liu H; Wang Z; Lei T; Li Y; Hou T
RNA; 2018 Sep; 24(9):1183-1194. PubMed ID: 29930024
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.
Sun H; Li Y; Shen M; Tian S; Xu L; Pan P; Guan Y; Hou T
Phys Chem Chem Phys; 2014 Oct; 16(40):22035-45. PubMed ID: 25205360
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. 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]
8. Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set.
Sun H; Li Y; Tian S; Xu L; Hou T
Phys Chem Chem Phys; 2014 Aug; 16(31):16719-29. PubMed ID: 24999761
[TBL] [Abstract][Full Text] [Related]
9. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4.
El Khoury L; Santos-Martins D; Sasmal S; Eberhardt J; Bianco G; Ambrosio FA; Solis-Vasquez L; Koch A; Forli S; Mobley DL
J Comput Aided Mol Des; 2019 Dec; 33(12):1011-1020. PubMed ID: 31691919
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. 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]
12. 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]
13. 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]
14. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
Wang E; Sun H; Wang J; Wang Z; Liu H; Zhang JZH; Hou T
Chem Rev; 2019 Aug; 119(16):9478-9508. PubMed ID: 31244000
[TBL] [Abstract][Full Text] [Related]
15. Improving virtual screening results with MM/GBSA and MM/PBSA rescoring.
Sahakyan H
J Comput Aided Mol Des; 2021 Jun; 35(6):731-736. PubMed ID: 33983518
[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. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.
Rastelli G; Del Rio A; Degliesposti G; Sgobba M
J Comput Chem; 2010 Mar; 31(4):797-810. PubMed ID: 19569205
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.
Yau MQ; Emtage AL; Chan NJY; Doughty SW; Loo JSE
J Comput Aided Mol Des; 2019 May; 33(5):487-496. PubMed ID: 30989574
[TBL] [Abstract][Full Text] [Related]
20. dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.
Spiliotopoulos D; Kastritis PL; Melquiond AS; Bonvin AM; Musco G; Rocchia W; Spitaleri A
Front Mol Biosci; 2016; 3():46. PubMed ID: 27630991
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
