(Q37411726)

20 August 2017

Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons (English)

1 reference

20 August 2017

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Chuanyun Xiao

1

1 reference

20 August 2017

Yingkai Zhang

series ordinal

2

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20 August 2017

language of work or name

English

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publication date

1 September 2007

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Journal of Chemical Physics

20 August 2017

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20 August 2017

127

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20 August 2017

12

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20 August 2017

124102

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Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Electrostatic basis for enzyme catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Mechanisms and free energies of enzymatic reactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Modelling enzyme reaction mechanisms, specificity and catalysis.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Quantum mechanical methods for enzyme kinetics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Density-functional exchange-energy approximation with correct asymptotic behavior

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Simulating enzyme reactions: challenges and perspectives

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Variational optimization of effective atom centered potentials for molecular properties

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Simple minimum principle to derive a quantum-mechanical/molecular-mechanical method

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773247

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

2 September 2018

1 reference

Stochastic fluctuations and chiral symmetry breaking: exact solution of Lente model

21 January 2018

1 reference

Pseudopotentials that work: From H to Pu

21 January 2018

1 reference

Inhomogeneous Electron Gas

21 January 2018

1 reference

Norm-Conserving Pseudopotentials

21 January 2018

1 reference

The SIESTA method forab initioorder-Nmaterials simulation

21 January 2018

1 reference

QM/MM Methods for Biological Systems

21 January 2018

1 reference

QM/MM: what have we learned, where are we, and where do we go from here?

21 January 2018

1 reference

QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis

21 January 2018

1 reference

Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches

21 January 2018

1 reference

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method

21 January 2018

1 reference

Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics

21 January 2018

1 reference

Adjusted Connection Atoms for Combined Quantum Mechanical and Molecular Mechanical Methods

21 January 2018

1 reference

Multicentered valence electron effective potentials: A solution to the link atom problem for ground and excited electronic states

21 January 2018

1 reference

Systematic generation of finite-range atomic basis sets for linear-scaling calculations

21 January 2018

1 reference

Numerical atomic orbitals for linear-scaling calculations

21 January 2018

1 reference

A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method

21 January 2018

1 reference

12 December 2020

Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study

1 reference

12 December 2020

Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein

1 reference

12 December 2020

Efficient pseudopotentials for plane-wave calculations

1 reference

12 December 2020

Self-consistent order-N density-functional calculations for very large systems

1 reference

12 December 2020

Efficient silicon surface and cluster modeling using quantum capping potentials

1 reference

12 December 2020

Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.2774980

1 reference

20 August 2017

1 reference

20 August 2017

PubMed publication ID

17902888

1 reference