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.
1390 related articles for article (PubMed ID: 26605738)
1. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. Miller BR; McGee TD; Swails JM; Homeyer N; Gohlke H; Roitberg AE J Chem Theory Comput; 2012 Sep; 8(9):3314-21. PubMed ID: 26605738 [TBL] [Abstract][Full Text] [Related]
2. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Valdés-Tresanco MS; Valdés-Tresanco ME; Valiente PA; Moreno E J Chem Theory Comput; 2021 Oct; 17(10):6281-6291. PubMed ID: 34586825 [TBL] [Abstract][Full Text] [Related]
3. Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study. Aldeghi M; Bodkin MJ; Knapp S; Biggin PC J Chem Inf Model; 2017 Sep; 57(9):2203-2221. PubMed ID: 28786670 [TBL] [Abstract][Full Text] [Related]
5. 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]
6. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Vorobjev YN; Almagro JC; Hermans J Proteins; 1998 Sep; 32(4):399-413. PubMed ID: 9726412 [TBL] [Abstract][Full Text] [Related]
7. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Pitera JW; Kollman PA Proteins; 2000 Nov; 41(3):385-97. PubMed ID: 11025549 [TBL] [Abstract][Full Text] [Related]
8. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. Shivakumar D; Deng Y; Roux B J Chem Theory Comput; 2009 Apr; 5(4):919-30. PubMed ID: 26609601 [TBL] [Abstract][Full Text] [Related]
9. Theoretical determination of the standard reduction potentials of pheophytin-a in N,N-dimethyl formamide and membrane. Mehta N; Datta SN J Phys Chem B; 2007 Jun; 111(25):7210-7. PubMed ID: 17536851 [TBL] [Abstract][Full Text] [Related]
10. Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant. Akkus E; Tayfuroglu O; Yildiz M; Kocak A J Phys Chem B; 2023 May; 127(20):4415-4429. PubMed ID: 37171911 [TBL] [Abstract][Full Text] [Related]
11. Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions. Brice AR; Dominy BN J Comput Chem; 2011 May; 32(7):1431-40. PubMed ID: 21284003 [TBL] [Abstract][Full Text] [Related]
12. Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site. Fox SJ; Dziedzic J; Fox T; Tautermann CS; Skylaris CK Proteins; 2014 Dec; 82(12):3335-46. PubMed ID: 25212393 [TBL] [Abstract][Full Text] [Related]
13. Efficient Generalized Born Models for Monte Carlo Simulations. Michel J; Taylor RD; Essex JW J Chem Theory Comput; 2006 May; 2(3):732-9. PubMed ID: 26626678 [TBL] [Abstract][Full Text] [Related]
14. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Archontis G; Simonson T; Karplus M J Mol Biol; 2001 Feb; 306(2):307-27. PubMed ID: 11237602 [TBL] [Abstract][Full Text] [Related]
15. 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]
16. Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007). Hafner J J Phys Condens Matter; 2008 Feb; 20(6):060301. PubMed ID: 21693862 [TBL] [Abstract][Full Text] [Related]
17. 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]