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.
134 related articles for article (PubMed ID: 22462848)
1. Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. Pham TT; Shirts MR J Chem Phys; 2012 Mar; 136(12):124120. PubMed ID: 22462848 [TBL] [Abstract][Full Text] [Related]
2. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase. Pham TT; Shirts MR J Chem Phys; 2011 Jul; 135(3):034114. PubMed ID: 21786994 [TBL] [Abstract][Full Text] [Related]
3. Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites. Naden LN; Pham TT; Shirts MR J Chem Theory Comput; 2014 Mar; 10(3):1128-49. PubMed ID: 26580188 [TBL] [Abstract][Full Text] [Related]
4. Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions. Blondel A J Comput Chem; 2004 May; 25(7):985-93. PubMed ID: 15027110 [TBL] [Abstract][Full Text] [Related]
5. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface. Hu H; Lu Z; Parks JM; Burger SK; Yang W J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486 [TBL] [Abstract][Full Text] [Related]
6. Linear-scaling soft-core scheme for alchemical free energy calculations. Buelens FP; Grubmüller H J Comput Chem; 2012 Jan; 33(1):25-33. PubMed ID: 21953650 [TBL] [Abstract][Full Text] [Related]
7. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations. Gapsys V; Seeliger D; de Groot BL J Chem Theory Comput; 2012 Jul; 8(7):2373-82. PubMed ID: 26588970 [TBL] [Abstract][Full Text] [Related]
8. Direct determination of reaction paths and stationary points on potential of mean force surfaces. Li G; Cui Q J Mol Graph Model; 2005 Oct; 24(2):82-93. PubMed ID: 16005650 [TBL] [Abstract][Full Text] [Related]
9. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. Liu H; Lu Z; Cisneros GA; Yang W J Chem Phys; 2004 Jul; 121(2):697-706. PubMed ID: 15260596 [TBL] [Abstract][Full Text] [Related]
11. Accurate vibrational-rotational partition functions and standard-state free energy values for H2O2 from Monte Carlo path-integral calculations. Lynch VA; Mielke SL; Truhlar DG J Chem Phys; 2004 Sep; 121(11):5148-62. PubMed ID: 15352807 [TBL] [Abstract][Full Text] [Related]
12. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. Lu N; Kofke DA; Woolf TB J Comput Chem; 2004 Jan; 25(1):28-39. PubMed ID: 14634991 [TBL] [Abstract][Full Text] [Related]
13. Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions. Naden LN; Shirts MR J Chem Theory Comput; 2015 Jun; 11(6):2536-49. PubMed ID: 26575553 [TBL] [Abstract][Full Text] [Related]
14. The parameterization and validation of generalized born models using the pairwise descreening approximation. Michel J; Taylor RD; Essex JW J Comput Chem; 2004 Nov; 25(14):1760-70. PubMed ID: 15362133 [TBL] [Abstract][Full Text] [Related]
15. Tracing the minimum-energy path on the free-energy surface. Fleurat-Lessard P; Ziegler T J Chem Phys; 2005 Aug; 123(8):084101. PubMed ID: 16164276 [TBL] [Abstract][Full Text] [Related]
16. Accurate free energy calculation along optimized paths. Chen C; Xiao Y J Comput Chem; 2010 May; 31(7):1368-75. PubMed ID: 19859916 [TBL] [Abstract][Full Text] [Related]
17. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Sham YY; Chu ZT; Tao H; Warshel A Proteins; 2000 Jun; 39(4):393-407. PubMed ID: 10813821 [TBL] [Abstract][Full Text] [Related]
18. Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method. Bruckner S; Boresch S J Comput Chem; 2011 May; 32(7):1303-19. PubMed ID: 21425288 [TBL] [Abstract][Full Text] [Related]
19. Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration. Bruckner S; Boresch S J Comput Chem; 2011 May; 32(7):1320-33. PubMed ID: 21425289 [TBL] [Abstract][Full Text] [Related]
20. The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation. Das A; Andersen HC J Chem Phys; 2009 Jul; 131(3):034102. PubMed ID: 19624176 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]