128 related articles for article (PubMed ID: 26627439)
21. Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.
Dieterich JM; Werner HJ; Mata RA; Metz S; Thiel W
J Chem Phys; 2010 Jan; 132(3):035101. PubMed ID: 20095751
[TBL] [Abstract][Full Text] [Related]
22. Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface.
Doron D; Major DT; Kohen A; Thiel W; Wu X
J Chem Theory Comput; 2011 Oct; 7(10):3420-37. PubMed ID: 26598171
[TBL] [Abstract][Full Text] [Related]
23. 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]
24. Mechanistic aspects of propene epoxidation by hydrogen peroxide. Catalytic role of water molecules, external electric field, and zeolite framework of TS-1.
Stare J; Henson NJ; Eckert J
J Chem Inf Model; 2009 Apr; 49(4):833-46. PubMed ID: 19267473
[TBL] [Abstract][Full Text] [Related]
25. Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin.
Hermann JC; Hensen C; Ridder L; Mulholland AJ; Höltje HD
J Am Chem Soc; 2005 Mar; 127(12):4454-65. PubMed ID: 15783228
[TBL] [Abstract][Full Text] [Related]
26. A definitive mechanism for chorismate mutase.
Zhang X; Zhang X; Bruice TC
Biochemistry; 2005 Aug; 44(31):10443-8. PubMed ID: 16060652
[TBL] [Abstract][Full Text] [Related]
27. 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]
28. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.
Hori K; Yamaguchi T; Uezu K; Sumimoto M
J Comput Chem; 2011 Apr; 32(5):778-86. PubMed ID: 21341291
[TBL] [Abstract][Full Text] [Related]
29. QM/MM-PBSA method to estimate free energies for reactions in proteins.
Kaukonen M; Söderhjelm P; Heimdal J; Ryde U
J Phys Chem B; 2008 Oct; 112(39):12537-48. PubMed ID: 18781715
[TBL] [Abstract][Full Text] [Related]
30. Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions.
Pang J; Pu J; Gao J; Truhlar DG; Allemann RK
J Am Chem Soc; 2006 Jun; 128(24):8015-23. PubMed ID: 16771517
[TBL] [Abstract][Full Text] [Related]
31. Peptide hydrolysis catalyzed by matrix metalloproteinase 2: a computational study.
Díaz N; Suárez D
J Phys Chem B; 2008 Jul; 112(28):8412-24. PubMed ID: 18570467
[TBL] [Abstract][Full Text] [Related]
32. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.
Fox SJ; Pittock C; Tautermann CS; Fox T; Christ C; Malcolm NO; Essex JW; Skylaris CK
J Phys Chem B; 2013 Aug; 117(32):9478-85. PubMed ID: 23841453
[TBL] [Abstract][Full Text] [Related]
33. Transition-state characterization of the ammonia ionization process in aqueous solution via the free-energy gradient method.
Nagaoka M; Nagae Y; Koyano Y; Oishi Y
J Phys Chem A; 2006 Apr; 110(13):4555-63. PubMed ID: 16571063
[TBL] [Abstract][Full Text] [Related]
34. How dihydrofolate reductase facilitates protonation of dihydrofolate.
Rod TH; Brooks CL
J Am Chem Soc; 2003 Jul; 125(29):8718-9. PubMed ID: 12862454
[TBL] [Abstract][Full Text] [Related]
35. Free energy simulations of active-site mutants of dihydrofolate reductase.
Doron D; Stojković V; Gakhar L; Vardi-Kilshtain A; Kohen A; Major DT
J Phys Chem B; 2015 Jan; 119(3):906-16. PubMed ID: 25382260
[TBL] [Abstract][Full Text] [Related]
36. Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process.
Ishida T; Kato S
J Am Chem Soc; 2003 Oct; 125(39):12035-48. PubMed ID: 14505425
[TBL] [Abstract][Full Text] [Related]
37. A multilayered-representation, quantum mechanical/molecular mechanics study of the CH(3)Cl + F(-) reaction in aqueous solution: the reaction mechanism, solvent effects and potential of mean force.
Zhang J; Xu Y; Chen J; Wang D
Phys Chem Chem Phys; 2014 Apr; 16(16):7611-7. PubMed ID: 24637944
[TBL] [Abstract][Full Text] [Related]
38. High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase.
Kaiyawet N; Lonsdale R; Rungrotmongkol T; Mulholland AJ; Hannongbua S
J Chem Theory Comput; 2015 Feb; 11(2):713-22. PubMed ID: 26579604
[TBL] [Abstract][Full Text] [Related]
39. Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study.
Ibrahim MA
J Chem Inf Model; 2011 Oct; 51(10):2549-59. PubMed ID: 21942911
[TBL] [Abstract][Full Text] [Related]
40. Simulation of the enzyme reaction mechanism of malate dehydrogenase.
Cunningham MA; Ho LL; Nguyen DT; Gillilan RE; Bash PA
Biochemistry; 1997 Apr; 36(16):4800-16. PubMed ID: 9125501
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]
