Computational enzymology

Current Opinion in Chemical Biology

Volumn 4, Issue 5, 2000, Pages 540-544

  Bruice, Thomas C ^a   Kahn, Kalju ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERISM; CHEMICAL REACTION; ENZYME MECHANISM; ENZYME SUBSTRATE; ENZYMOLOGY; MOLECULAR DYNAMICS; PREDICTION; PROTEIN ANALYSIS; QUANTUM MECHANICS; REVIEW; THEORY; THERMODYNAMICS;

EID: 0033780353     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(00)00129-0     Document Type: Review

References (65)

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3. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
4. All-atom empirical potential for molecular modeling and dynamics studies of proteins
5. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
6. Importance of correlated motions in forming highly reactive near attack conformations in catechol O-methyltransferase
7. Active site dynamics of the Hhal methyltransferase: Insights from computer simulation
8. - from 1,2-dichloroethane at the active site of Xanthobacter autotrophicus haloalkane dehalogenase
9. + in the active site of formate dehydrogenase
10. The mechanism of phosphodiester hydrolysis: Near in-line attack conformations in the hammerhead ribozyme
11. Ground state and transition state contributions to the rates of intramolecular and enzymatic reactions
12. Chemical basis for enzyme catalysis
13. A model study of the enzyme-catalyzed cytosine methylation using ab initio quantum mechanical and density functional theory calculations: pK(a) of the cytosine N3 in the intermediates and transition states of the reaction
14. A theoretical examination of the factors controlling the catalytic efficiency of a transmethylation enzyme: Catechol O-methyltransferase
15. Transition-state and ground-state structures and their interaction with the active-site residues in catechol O-methyltransferase
16. QM-FE and molecular dynamics calculations on catechol O-methyltransferase: Free energy of activation in the enzyme and in aqueous solution and regioselectivity of the enzyme-catalyzed reaction
17. QM and QM-FE simulations on reactions of relevance to enzyme catalysis: Trypsin, catechol O-methyltransferase, beta-lactamase and pseudouridine synthase
18. Accurate ab initio calculations on large van der Waals clusters
19. Basis set superposition error
20. How does basis set superposition error change the potential surfaces for hydrogen bonded dimers?
21. Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods
22. Large scale ab initio quantum chemical calculation of the intermediates in the soluble methane monooxygenase catalytic cycle
23. Correlated ab initio electronic structure calculations for large molecules
24. Fast, accurate semiempirical molecular orbital calculations for macromolecules
25. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions
26. Methods and applications of combined quantum mechanical and molecular mechanical potentials
27. Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase
28. Catalytic mechanism of dihydrofolate reductase enzyme. A combined quantum-mechanical/molecular-mechanical characterization of transition state structure for the hydride transfer step
29. Transition state structure invariance to model system size and calculation levels: A QM/MM study of the carboxylation step catalyzed by Rubisco
30. Transition-state structural refinement with GRACE and CHARMM: Realistic modelling of lactate dehydrogenase using a combined quantum/classical method
31. Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase
32. Modelling the catalytic reaction in human aldose reductase
33. AM1: A new general purpose quantum mechanical molecular model
34. Optimization of parameters for semiempirical methods I. Method
35. Optimization of parameters for semiempirical methods. II. Applications
36. Critical test of PM3 calculated gas-phase acidities
37. Critical test of PM3-calculated proton transfer activation energies: A comparison with ab initio and AM1 calculations
38. Some difficulties encountered with AM1 and PM3 calculations
39. Charge transfer in biologically important molecules: Comparison of high-level ab initio and semiempirical methods
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42. Frontier bonds in QM/MM methods: A comparison of different approaches
43. Quantum chemical computations on parts of large molecules - The ab initio local self consistent field method
44. A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations
45. A hybrid QM-MM potential employing Hartree-Fock or density functional methods in the quantum region
46. A hybrid density functional theory molecular mechanics study of nickel-iron hydrogenase: Investigation of the active site redox states
47. Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved
48. Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations
49. Computer simulations for chemical reactions in solution
50. Theoretical examination of the S(N)2 reaction involving chloride ion and methyl chloride in the gas phase and aqueous solution
51. Combined ab initio and free energy calculations to study reactions in enzymes and solution: Amide hydrolysis in trypsin and aqueous solution
52. Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
53. Is there a covalent intermediate in the viral neuraminidase reaction? A hybrid potential free-energy study
54. Walden-inversion-enforced transition-state stabilization in a protein tyrosine phosphatase
55. Electrostatic stress in catalysis: Structure and mechanism of the enzyme orotidine monophosphate decarboxylase
56. Hybrid ab initio quantum mechanics molecular mechanics calculations of free energy surfaces for enzymatic reactions: The nucleophilic attack in subtilisin
57. Origin of the catalytic power of acetylcholinesterase: Computer simulation studies
58. Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of glyoxalase I catalyzed reaction
59. How does GAP catalyze the GTPase reaction of Ras?: A computer simulation study
60. QM/MM boundaries across covalent bonds: A frozen localized molecular orbital-based approach for the effective fragment potential method
61. The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
62. Ab initio hybrid quantum mechanical/molecular mechanical studies of the mechanisms of the enzymes protein kinase and thymidine phosphorylase
63. How is the active site of enolase organized to catalyze two different reaction steps?