Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. - Wikidata - wikimedia - TriplyDB

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.

http://www.wikidata.org/entity/Q38770768

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Role of substrate dynamics in protein prenylation reactions Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery A sugar isomerization reaction established on various (βα)₈-barrel scaffolds is based on substrate-assisted catalysis A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations Carbinolamine formation and dehydration in a DNA repair enzyme active site Unraveling 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 inhibitor Density-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 tables Free 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 fields Simulating 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 T New QM/MM implementation of the DFTB3 method in the gromacs package Mechanistic insight into the reaction catalysed by bacterial type II dehydroquinases

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P2860

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.

http://www.wikidata.org/entity/Q38770768

description

2007 nî lūn-bûn

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2007年の論文

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2007年論文

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2007年論文

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2007年論文

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2007年論文

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2007年論文

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2007年论文

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2007年论文

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2007年论文

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name

Implementation of the SCC-DFTB ...... er molecular dynamics package.

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type

label

Implementation of the SCC-DFTB ...... er molecular dynamics package.

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prefLabel

Implementation of the SCC-DFTB ...... er molecular dynamics package.

@en

P1433

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P1433

Journal of Physical Chemistry A

P1476

Implementation of the SCC-DFTB ...... er molecular dynamics package.

@en

P2093

Adrian E Roitberg

http://www.w3.org/2001/XMLSchema#string

David A Case

http://www.w3.org/2001/XMLSchema#string

Gustavo de M Seabra

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Marcus Elstner

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Ross C Walker

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P2860

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

The Amber biomolecular simulation programs

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.

Intrinsic backbone preferences are fully present in blocked amino acids

Conformational preferences of non-prolyl and prolyl residues.

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5655-5664

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scholarly article

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10.1021/JP070071L

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26

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111

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2007-05-24T00:00:00Z

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6311987

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17521173

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3197852

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