These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
274 related articles for article (PubMed ID: 22817270)
1. The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant. Genheden S; Kuhn O; Mikulskis P; Hoffmann D; Ryde U J Chem Inf Model; 2012 Aug; 52(8):2079-88. PubMed ID: 22817270 [TBL] [Abstract][Full Text] [Related]
2. Can MM/GBSA calculations be sped up by system truncation? Misini Ignjatović M; Mikulskis P; Söderhjelm P; Ryde U J Comput Chem; 2018 Mar; 39(7):361-372. PubMed ID: 29178493 [TBL] [Abstract][Full Text] [Related]
3. Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model. Kopitz H; Cashman DA; Pfeiffer-Marek S; Gohlke H J Comput Chem; 2012 Apr; 33(9):1004-13. PubMed ID: 22298332 [TBL] [Abstract][Full Text] [Related]
4. Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA. Genheden S; Nilsson I; Ryde U J Chem Inf Model; 2011 Apr; 51(4):947-58. PubMed ID: 21417269 [TBL] [Abstract][Full Text] [Related]
5. 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]
6. 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]
7. Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations. Lepsík M; Kríz Z; Havlas Z Proteins; 2004 Nov; 57(2):279-93. PubMed ID: 15340915 [TBL] [Abstract][Full Text] [Related]
8. 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]
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. A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections. Mikulskis P; Genheden S; Wichmann K; Ryde U J Comput Chem; 2012 May; 33(12):1179-89. PubMed ID: 22396176 [TBL] [Abstract][Full Text] [Related]
11. Will molecular dynamics simulations of proteins ever reach equilibrium? Genheden S; Ryde U Phys Chem Chem Phys; 2012 Jun; 14(24):8662-77. PubMed ID: 22614001 [TBL] [Abstract][Full Text] [Related]
12. MM/GBSA binding energy prediction on the PDBbind data set: successes, failures, and directions for further improvement. Greenidge PA; Kramer C; Mozziconacci JC; Wolf RM J Chem Inf Model; 2013 Jan; 53(1):201-9. PubMed ID: 23268595 [TBL] [Abstract][Full Text] [Related]
13. 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]
14. 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]
15. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations. Godschalk F; Genheden S; Söderhjelm P; Ryde U Phys Chem Chem Phys; 2013 May; 15(20):7731-9. PubMed ID: 23595060 [TBL] [Abstract][Full Text] [Related]
16. E-novo: an automated workflow for efficient structure-based lead optimization. Pearce BC; Langley DR; Kang J; Huang H; Kulkarni A J Chem Inf Model; 2009 Jul; 49(7):1797-809. PubMed ID: 19552372 [TBL] [Abstract][Full Text] [Related]
17. 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]
18. Structural parameterization of the binding enthalpy of small ligands. Luque I; Freire E Proteins; 2002 Nov; 49(2):181-90. PubMed ID: 12210999 [TBL] [Abstract][Full Text] [Related]
19. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding. Thorsteinsdottir HB; Schwede T; Zoete V; Meuwly M Proteins; 2006 Nov; 65(2):407-23. PubMed ID: 16941468 [TBL] [Abstract][Full Text] [Related]
20. Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? Manzoni F; Uranga J; Genheden S; Ryde U J Chem Inf Model; 2017 Nov; 57(11):2865-2873. PubMed ID: 29076739 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]