395 related articles for article (PubMed ID: 23789789)
1. 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]
2. 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]
3. 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]
4. 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]
5. 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]
6. 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]
7. Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease.
Oehme DP; Brownlee RT; Wilson DJ
J Comput Chem; 2012 Dec; 33(32):2566-80. PubMed ID: 22915442
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. 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]
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 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]
12. 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]
13. Mapping the binding site of a large set of quinazoline type EGF-R inhibitors using molecular field analyses and molecular docking studies.
Hou T; Zhu L; Chen L; Xu X
J Chem Inf Comput Sci; 2003; 43(1):273-87. PubMed ID: 12546563
[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. 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]
16. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
Genheden S; Ryde U
Proteins; 2012 May; 80(5):1326-42. PubMed ID: 22274991
[TBL] [Abstract][Full Text] [Related]
17. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Genheden S; Ryde U
Expert Opin Drug Discov; 2015 May; 10(5):449-61. PubMed ID: 25835573
[TBL] [Abstract][Full Text] [Related]
18. Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N.
Vorontsov II; Miyashita O
J Comput Chem; 2011 Apr; 32(6):1043-53. PubMed ID: 20949512
[TBL] [Abstract][Full Text] [Related]
19. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.
Cino EA; Choy WY; Karttunen M
J Chem Theory Comput; 2012 Aug; 8(8):2725-2740. PubMed ID: 22904695
[TBL] [Abstract][Full Text] [Related]
20. Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening.
Virtanen SI; Niinivehmas SP; Pentikäinen OT
J Mol Graph Model; 2015 Nov; 62():303-318. PubMed ID: 26550792
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]