Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.
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Role of substrate dynamics in protein prenylation reactionsSolution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methodsSolution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated AllosteryA sugar isomerization reaction established on various (βα)₈-barrel scaffolds is based on substrate-assisted catalysisA catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulationsCarbinolamine formation and dehydration in a DNA repair enzyme active siteUnraveling the differences of the hydrolytic activity of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase: a quantum mechanics-molecular mechanics modeling study.An extensible interface for QM/MM molecular dynamics simulations with AMBER.Catalysis of carboxypeptidase A: promoted-water versus nucleophilic pathways.Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitorDensity-functional expansion methods: generalization of the auxiliary basis.The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families.Simulations of allosteric motions in the zinc sensor CzrA.Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations.Spherical tensor gradient operator method for integral rotation: a simple, efficient, and extendable alternative to Slater-Koster tablesFree energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate.Biological applications of hybrid quantum mechanics/molecular mechanics calculation.A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: application to (C6H6)(+/0)Ar(n) clusters.Polarization effects in molecular mechanical force fieldsSimulating the inhibition reaction of Mycobacterium tuberculosis L,D-transpeptidase 2 by carbapenems.Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study.Refined models of New Delhi metallo-beta-lactamase-1 with inhibitors: an QM/MM modeling study.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.Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase.Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters.Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations.Density functional tight binding.Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding.Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.Redistribution of carbonyl stretch mode energy in isolated and solvated N-methylacetamide: kinetic energy spectral density analyses.L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.Structure and energy based quantitative missense variant effect analysis provides insights into drug resistance mechanisms of anaplastic lymphoma kinase mutations.Fluorescent dyes in the context of DNA-binding: The case of Thioflavin TNew QM/MM implementation of the DFTB3 method in the gromacs packageMechanistic insight into the reaction catalysed by bacterial type II dehydroquinases
P2860
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P2860
Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.
description
2007 nî lūn-bûn
@nan
2007年の論文
@ja
2007年論文
@yue
2007年論文
@zh-hant
2007年論文
@zh-hk
2007年論文
@zh-mo
2007年論文
@zh-tw
2007年论文
@wuu
2007年论文
@zh
2007年论文
@zh-cn
name
Implementation of the SCC-DFTB ...... er molecular dynamics package.
@en
type
label
Implementation of the SCC-DFTB ...... er molecular dynamics package.
@en
prefLabel
Implementation of the SCC-DFTB ...... er molecular dynamics package.
@en
P2093
P2860
P356
P1476
Implementation of the SCC-DFTB ...... er molecular dynamics package.
@en
P2093
Adrian E Roitberg
David A Case
Gustavo de M Seabra
Marcus Elstner
Ross C Walker
P2860
P304
P356
10.1021/JP070071L
P407
P577
2007-05-24T00:00:00Z