397 related articles for article (PubMed ID: 33213150)
1. How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations?
Hao D; He X; Ji B; Zhang S; Wang J
J Chem Inf Model; 2020 Dec; 60(12):6624-6633. PubMed ID: 33213150
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. 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]
4. 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]
5. 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]
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. Free energy calculations to estimate ligand-binding affinities in structure-based drug design.
Reddy MR; Reddy CR; Rathore RS; Erion MD; Aparoy P; Reddy RN; Reddanna P
Curr Pharm Des; 2014; 20(20):3323-37. PubMed ID: 23947646
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. 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]
10. Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and End-Point Methods.
Nixon MG; Fadda E
Methods Mol Biol; 2019; 2039():229-242. PubMed ID: 31342430
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. 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]
13. 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]
14. 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]
15. Accuracy and precision of binding free energy prediction for a tacrine related lead inhibitor of acetylcholinesterase with an arsenal of supercomputerized molecular modelling methods: a comparative study.
Dolezal R
J Biomol Struct Dyn; 2022; 40(21):11291-11319. PubMed ID: 34323654
[TBL] [Abstract][Full Text] [Related]
16. Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method.
Sun Y; He X; Hou T; Cai L; Man VH; Wang J
J Comput Chem; 2023 May; 44(14):1334-1346. PubMed ID: 36807356
[TBL] [Abstract][Full Text] [Related]
17. Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening.
Yang M; Bo Z; Xu T; Xu B; Wang D; Zheng H
Brief Bioinform; 2023 Jul; 24(4):. PubMed ID: 37328705
[TBL] [Abstract][Full Text] [Related]
18. Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors.
Lima Silva WJ; Ferreira de Freitas R
J Comput Aided Mol Des; 2023 Sep; 37(9):407-418. PubMed ID: 37378817
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. 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]
[Next] [New Search]