279 related articles for article (PubMed ID: 22916168)
1. An efficient computational method for calculating ligand binding affinities.
Suenaga A; Okimoto N; Hirano Y; Fukui K
PLoS One; 2012; 7(8):e42846. PubMed ID: 22916168
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. 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]
5. Improving docking results via reranking of ensembles of ligand poses in multiple X-ray protein conformations with MM-GBSA.
Greenidge PA; Kramer C; Mozziconacci JC; Sherman W
J Chem Inf Model; 2014 Oct; 54(10):2697-717. PubMed ID: 25266271
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
Misini Ignjatović M; Caldararu O; Dong G; Muñoz-Gutierrez C; Adasme-Carreño F; Ryde U
J Comput Aided Mol Des; 2016 Sep; 30(9):707-730. PubMed ID: 27565797
[TBL] [Abstract][Full Text] [Related]
8. 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]
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. Template-Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands.
Raman EP
J Chem Inf Model; 2019 Jun; 59(6):2690-2701. PubMed ID: 31045363
[TBL] [Abstract][Full Text] [Related]
11. Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?
Mulakala C; Viswanadhan VN
J Mol Graph Model; 2013 Nov; 46():41-51. PubMed ID: 24121518
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations.
Wang E; Fu W; Jiang D; Sun H; Wang J; Zhang X; Weng G; Liu H; Tao P; Hou T
J Chem Inf Model; 2021 Jun; 61(6):2844-2856. PubMed ID: 34014672
[TBL] [Abstract][Full Text] [Related]
14. Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized Born surface area rescoring to improve enrichment.
Zhang X; Wong SE; Lightstone FC
J Chem Inf Model; 2014 Jan; 54(1):324-37. PubMed ID: 24358939
[TBL] [Abstract][Full Text] [Related]
15. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.
Izadi S; Aguilar B; Onufriev AV
J Chem Theory Comput; 2015 Sep; 11(9):4450-9. PubMed ID: 26575935
[TBL] [Abstract][Full Text] [Related]
16. Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction.
Yang CY; Sun H; Chen J; Nikolovska-Coleska Z; Wang S
J Am Chem Soc; 2009 Sep; 131(38):13709-21. PubMed ID: 19736924
[TBL] [Abstract][Full Text] [Related]
17. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities.
Wang E; Liu H; Wang J; Weng G; Sun H; Wang Z; Kang Y; Hou T
J Chem Inf Model; 2020 Nov; 60(11):5353-5365. PubMed ID: 32175734
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations.
Ben-Shalom IY; Pfeiffer-Marek S; Baringhaus KH; Gohlke H
J Chem Inf Model; 2017 Feb; 57(2):170-189. PubMed ID: 27996253
[TBL] [Abstract][Full Text] [Related]
20. 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]
[Next] [New Search]