Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.
about
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutationsMetal Ion Modeling Using Classical MechanicsNMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations.Intrinsic proton-donating power of zinc-bound water in a carbonic anhydrase active site model estimated by NMR.An implicit solvent model for SCC-DFTB with Charge-Dependent Radii.Catalysis of carboxypeptidase A: promoted-water versus nucleophilic pathways.Clarification of the mechanism of acylation reaction and origin of substrate specificity of the serine-carboxyl peptidase sedolisin through QM/MM free energy simulationsParametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applicationsDensity-functional expansion methods: generalization of the auxiliary basis.Inhibitor and substrate binding by angiotensin-converting enzyme: quantum mechanical/molecular mechanical molecular dynamics studies.pH-Dependent reactivity for glycyl-L-tyrosine in carboxypeptidase-A-catalyzed hydrolysis.Combined quantum mechanical and molecular mechanical simulations of one- and two-electron reduction potentials of flavin cofactor in water, medium-chain acyl-CoA dehydrogenase, and cholesterol oxidaseA modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters.Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state.The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As.Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism.Long-distance proton transfer with a break in the bacteriorhodopsin active site.Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications.Strictly conserved lysine of prolyl-tRNA Synthetase editing domain facilitates binding and positioning of misacylated tRNA(Pro.).QM/MM X-ray refinement of zinc metalloenzymes.Effect of mutation on the stabilization energy of HIV-1 zinc fingers: a hybrid local self-consistent field/molecular mechanics investigation.Refined models of New Delhi metallo-beta-lactamase-1 with inhibitors: an QM/MM modeling study.Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS.DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB).A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins.Insights from QM/MM Modeling the 3D Structure of the 2009 H1N1 Influenza A Virus Neuraminidase and Its Binding Interactions with Antiviral Drugs.Catalytic mechanism of aromatic prenylation by NphB.Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide riboside quinone oxidoreductase 2.Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study.The catalytic role of glutamate 151 in the leucine aminopeptidase from Aeromonas proteolytica.Catalytic mechanism of class B2 metallo-beta-lactamase.QM/MM investigation of the catalytic mechanism of angiotensin-converting enzyme.Density functional tight binding.Analytical second-order geometrical derivatives of energy for the self-consistent-charge density-functional tight-binding method.
P2860
Q24649114-05AD12BF-D810-4FA2-9B25-FE5F83DDADE4Q30363020-3467F934-61B2-4FD9-ADC9-30D6EE2CDA61Q30880557-6F4E1178-43E9-41BD-ACFE-CA09CD9D18CFQ33935211-0BD0F9C6-843F-4169-857D-71F98CB6AC05Q34055062-B2370AF7-DB70-430F-A197-37A4BB3A036CQ34059864-26B20CDE-A175-4964-AF55-AFF56E6E640EQ34647803-5A602923-61BB-4C81-83B1-9CE8960CE80DQ35013411-933650B6-2C9B-453A-8790-63C3656BDBF4Q35040167-B0132FD7-9EB1-4E4D-8704-C5F548B3AB83Q35167293-D3289555-D92E-4098-AA12-E396DBF747BEQ35182011-C96CA10D-5322-4D5D-A031-0A4375F02F30Q35780064-67715111-B58F-41EA-B9D3-E22114E89681Q36487775-195191FD-E520-4789-8E94-931FE866EEF5Q36786982-FD476930-49C0-4E11-8107-7C30C82E1C68Q36843891-F0809E98-5B7A-4D6E-A5EB-39BE0640410FQ36870086-8DDF1354-7AE0-4D91-AE26-F8099D867E09Q36903666-3CE2B2D9-0796-49DE-BD4E-1C1B53E39E12Q37137337-7BDF325C-B27D-42C3-A423-727CB580A096Q37151359-3F1831C6-E260-4579-AD95-7CB626E9E8C3Q37309585-87CF694E-6D44-4D58-A5CE-8167FC5B328FQ37340639-D235ED75-FA87-41E2-AC01-012445B51C51Q37353692-EDFF5C09-6637-4579-98C8-40E6F5561805Q37372651-66449295-A8BD-4226-A8A0-8A51AC200AC6Q37701717-02C89CC8-8C5D-4C7C-B298-A4AF4E709E72Q38741646-7D489441-09C3-46FA-A315-D0FCF3DD8547Q39753228-DF5D2026-9116-4087-9F7A-9EF8F2151407Q40474115-FE299960-D620-4B77-9834-A904043A40D0Q40942612-7C663EF2-97AD-44D1-9DF0-5BFD2736F5FBQ41043204-4725BA37-C1F5-4493-AA60-19F9E8A3EE1CQ42073025-0C5A9406-3856-4AEA-8BF2-3E064890A4DFQ42150041-BDED93A9-24E4-41AD-ADDD-42AF85C95B88Q42234902-C8E7D90C-9A15-420B-8769-F3B7B6C3A820Q42563815-7B2A8663-417F-471F-93B0-7AF379936498Q42709596-9203DC93-AA58-47A2-8918-FA895856E7C4Q42928517-B13AFBB3-D62A-4B99-BF89-C6F91BCAE072Q44892453-B423D9A4-9A8D-47A1-8EEF-E5D0E2598AD5Q46901887-5DC364D2-E20C-4F01-8B51-5B9EAF8CF849Q50227932-79005D75-B5A0-411C-BA8B-95C692E3BAC9Q51113047-0352C565-71AE-4856-B02C-AF36BF00A9BDQ51635749-64E7F36A-F1CD-4EBD-9C5F-DFCE7DB215B1
P2860
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.
description
2003 nî lūn-bûn
@nan
2003年の論文
@ja
2003年学术文章
@wuu
2003年学术文章
@zh
2003年学术文章
@zh-cn
2003年学术文章
@zh-hans
2003年学术文章
@zh-my
2003年学术文章
@zh-sg
2003年學術文章
@yue
2003年學術文章
@zh-hant
name
Modeling zinc in biomolecules ...... ctural and energetic analysis.
@en
Modeling zinc in biomolecules ...... nsity functional tight binding
@nl
type
label
Modeling zinc in biomolecules ...... ctural and energetic analysis.
@en
Modeling zinc in biomolecules ...... nsity functional tight binding
@nl
prefLabel
Modeling zinc in biomolecules ...... ctural and energetic analysis.
@en
Modeling zinc in biomolecules ...... nsity functional tight binding
@nl
P2093
P356
P1476
Modeling zinc in biomolecules ...... ctural and energetic analysis.
@en
P2093
Efthimios Kaxiras
Marcus Elstner
Petra Munih
P304
P356
10.1002/JCC.10201
P577
2003-04-01T00:00:00Z