4.7 Article

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

Fitting molecular electrostatic potentials from quantum mechanical calculations

Hao Hu et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Chemistry, Multidisciplinary

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

Lihua Wang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Article Chemistry, Physical

QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase

Hao Hu et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Review Chemistry, Multidisciplinary

Mechanisms and free energies of enzymatic reactions

Jiali Gao et al.

CHEMICAL REVIEWS (2006)

Review Chemistry, Multidisciplinary

Electrostatic basis for enzyme catalysis

Arieh Warshel et al.

CHEMICAL REVIEWS (2006)

Article Chemistry, Physical

String method in collective variables: Minimum free energy paths and isocommittor surfaces

Luca Maragliano et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Multidisciplinary

Cope elimination: Elucidation of solvent effects from QM/MM simulations

Orlando Acevedo et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Multidisciplinary

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

C Corminboeuf et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Physical

Quadratic string method for determining the minimum-energy path based on multiobjective optimization

SK Burger et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

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

GA Cisneros et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2006)

Article Chemistry, Physical

Accurate QM/MM free energy calculations of enzyme reactions:: Methylation by catechol O-methyltransferase

TH Rod et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2005)

Article Biochemical Research Methods

Direct determination of reaction paths and stationary points on potential of mean force surfaces

GH Li et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2005)

Article Chemistry, Multidisciplinary

Covalent intermediates and enzyme proficiency

TC Bruice et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Chemistry, Physical

Tracing the minimum-energy path on the free-energy surface

P Fleurat-Lessard et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Chemistry, Physical

Dual-topology/dual-coordinate free-energy simulation using QM/MM force field

H Hu et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Chemistry, Physical

Optimizing the structures of minimum and transition state on the free energy surface

SY Yang et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2005)

Review Multidisciplinary Sciences

How enzymes work: Analysis by modern rate theory and computer simulations

M Garcia-Viloca et al.

SCIENCE (2004)

Article Chemistry, Multidisciplinary

Solute solvent dynamics and energetics in enzyme catalysis:: The SN2 reaction of dehalogenase as a general benchmark

MHM Olsson et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Chemistry, Multidisciplinary

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

GA Cisneros et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Biochemistry & Molecular Biology

Catalysis by enzyme conformational change as illustrated by orotidine 5′-monophosphate decarboxylase

JL Gao

CURRENT OPINION IN STRUCTURAL BIOLOGY (2003)

Review Chemistry, Multidisciplinary

The depth of chemical time and the power of enzymes as catalysts

R Wolfenden et al.

ACCOUNTS OF CHEMICAL RESEARCH (2001)

Article Chemistry, Physical

RISM-SCF study for the rated constant of SN2 reaction CH3Cl+Cl- in aqueous solution

K Ohmiya et al.

CHEMICAL PHYSICS LETTERS (2001)

Article Biochemistry & Molecular Biology

Quantum mechanics simulation of protein dynamics on long timescale

HY Liu et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2001)

Article Chemistry, Multidisciplinary

Triosephosphate isomerase: A theoretical comparison of alternative pathways

Q Cui et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

Article Chemistry, Multidisciplinary

How is the active site of enolase organized to catalyze two different reaction steps?

HY Liu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)

Review Chemistry, Physical

Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules

Q Cui et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2000)

Article Chemistry, Physical

Calculations of activation entropies of chemical reactions in solution

M Strajbl et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2000)

Article Chemistry, Physical

Structure optimization via free energy gradient method: Application to glycine zwitterion in aqueous solution

N Okuyama-Yoshida et al.

JOURNAL OF CHEMICAL PHYSICS (2000)