268 related articles for article (PubMed ID: 19405565)
1. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.
Zeng X; Hu H; Hu X; Yang W
J Chem Phys; 2009 Apr; 130(16):164111. PubMed ID: 19405565
[TBL] [Abstract][Full Text] [Related]
2. 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]
3. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
Lu Z; Yang W
J Chem Phys; 2004 Jul; 121(1):89-100. PubMed ID: 15260525
[TBL] [Abstract][Full Text] [Related]
4. QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.
Hu H; Lu Z; Yang W
J Chem Theory Comput; 2007 Mar; 3(2):390-406. PubMed ID: 19079734
[TBL] [Abstract][Full Text] [Related]
5. Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants.
Shen L; Zeng X; Hu H; Hu X; Yang W
J Chem Theory Comput; 2018 Sep; 14(9):4948-4957. PubMed ID: 30040901
[TBL] [Abstract][Full Text] [Related]
6. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.
Kamerlin SC; Haranczyk M; Warshel A
J Phys Chem B; 2009 Feb; 113(5):1253-72. PubMed ID: 19055405
[TBL] [Abstract][Full Text] [Related]
7. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
Rosta E; Klähn M; Warshel A
J Phys Chem B; 2006 Feb; 110(6):2934-41. PubMed ID: 16471904
[TBL] [Abstract][Full Text] [Related]
8. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.
Hu H; Yang W
Annu Rev Phys Chem; 2008; 59():573-601. PubMed ID: 18393679
[TBL] [Abstract][Full Text] [Related]
9. Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: a novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation.
Takahashi H; Ohno H; Kishi R; Nakano M; Matubayasi N
J Chem Phys; 2008 Nov; 129(20):205103. PubMed ID: 19045881
[TBL] [Abstract][Full Text] [Related]
10. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.
Kearns FL; Hudson PS; Boresch S; Woodcock HL
Methods Enzymol; 2016; 577():75-104. PubMed ID: 27498635
[TBL] [Abstract][Full Text] [Related]
11. Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies.
Reddy MR; Singh UC; Erion MD
J Comput Chem; 2007 Jan; 28(2):491-4. PubMed ID: 17186484
[TBL] [Abstract][Full Text] [Related]
12. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.
Zeng X; Hu H; Hu X; Cohen AJ; Yang W
J Chem Phys; 2008 Mar; 128(12):124510. PubMed ID: 18376946
[TBL] [Abstract][Full Text] [Related]
13. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
Xiang Y; Warshel A
J Phys Chem B; 2008 Jan; 112(3):1007-15. PubMed ID: 18166038
[TBL] [Abstract][Full Text] [Related]
14. Fragment quantum mechanical calculation of proteins and its applications.
He X; Zhu T; Wang X; Liu J; Zhang JZ
Acc Chem Res; 2014 Sep; 47(9):2748-57. PubMed ID: 24851673
[TBL] [Abstract][Full Text] [Related]
15. Facilitating
Snyder R; Kim B; Pan X; Shao Y; Pu J
Phys Chem Chem Phys; 2022 Oct; 24(41):25134-25143. PubMed ID: 36222412
[TBL] [Abstract][Full Text] [Related]
16. Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.
Shen L; Wu J; Yang W
J Chem Theory Comput; 2016 Oct; 12(10):4934-4946. PubMed ID: 27552235
[TBL] [Abstract][Full Text] [Related]
17. Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.
Plotnikov NV; Kamerlin SC; Warshel A
J Phys Chem B; 2011 Jun; 115(24):7950-62. PubMed ID: 21618985
[TBL] [Abstract][Full Text] [Related]
18. Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-.
Muller RP; Warshel A
Pac Symp Biocomput; 1996; ():524-38. PubMed ID: 9390256
[TBL] [Abstract][Full Text] [Related]
19. Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.
Shen L; Yang W
J Chem Theory Comput; 2018 Mar; 14(3):1442-1455. PubMed ID: 29438614
[TBL] [Abstract][Full Text] [Related]
20. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions.
Acevedo O; Jorgensen WL
Acc Chem Res; 2010 Jan; 43(1):142-51. PubMed ID: 19728702
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
