Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress.
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At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?Perspective: Defining and quantifying the role of dynamics in enzyme catalysisOn possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactionsFactors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactionsQuantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-C-phycocyaninEffects of a distal mutation on active site chemistry.Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthaseEnzyme homologues have distinct reaction paths through their transition states.Residue ionization in LpxC directly observed by 67Zn NMR spectroscopy.Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations.Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.Toward accurate screening in computer-aided enzyme design.Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase BCatalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: a comparison to analogous phosphatases.On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models.Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based modelsComparison of mode analyses at different resolutions applied to nucleic acid systems.Multiscale modeling of biological functions.On the relationship between thermal stability and catalytic power of enzymesThe entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects.Molecular dynamics: survey of methods for simulating the activity of proteins.Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogsQM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate IsomeraseHow do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations.Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions.Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.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 energiesBiomolecular simulation and modelling: status, progress and prospects.Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes.Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons.Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site.Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase.Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems.The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all
P2860
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P2860
Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress.
description
2003 nî lūn-bûn
@nan
2003年の論文
@ja
2003年論文
@yue
2003年論文
@zh-hant
2003年論文
@zh-hk
2003年論文
@zh-mo
2003年論文
@zh-tw
2003年论文
@wuu
2003年论文
@zh
2003年论文
@zh-cn
name
Structure/function correlation ...... itfalls, and current progress.
@ast
Structure/function correlation ...... itfalls, and current progress.
@en
type
label
Structure/function correlation ...... itfalls, and current progress.
@ast
Structure/function correlation ...... itfalls, and current progress.
@en
prefLabel
Structure/function correlation ...... itfalls, and current progress.
@ast
Structure/function correlation ...... itfalls, and current progress.
@en
P1476
Structure/function correlation ...... itfalls, and current progress.
@en
P2093
P304
P356
10.1016/S0065-3233(03)66007-9
P577
2003-01-01T00:00:00Z