QM/MM methods for biological systems
HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
H Hu, W Yang - Annu. Rev. Phys. Chem., 2008 - annualreviews.org
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an
accurate and efficient energetic description of complex chemical and biological systems …
accurate and efficient energetic description of complex chemical and biological systems …
Anisotropic, polarizable molecular mechanics studies of inter-and intramolecular interactions and ligand− macromolecule complexes. A bottom-up strategy
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is
formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical …
formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical …
Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
PEM Siegbahn, F Himo - JBIC Journal of Biological Inorganic Chemistry, 2009 - Springer
The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent
applications have used cluster models much larger than before which have given new …
applications have used cluster models much larger than before which have given new …
Multiscale quantum mechanics/molecular mechanics simulations with neural networks
Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics
(QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and …
(QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and …
QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: Application to an enzymatic reaction
We used the free-energy perturbation (FEP) method in quantum mechanics/molecular
mechanics (QM/MM) calculations to compute the free-energy profile of the hydroxylation …
mechanics (QM/MM) calculations to compute the free-energy profile of the hydroxylation …
Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods
Y Zhang - The Journal of chemical physics, 2005 - pubs.aip.org
The primary difficulties encountered in computational studies of chemical reactions in
macromolecules or solution stem from the need to describe chemical bond breaking/forming …
macromolecules or solution stem from the need to describe chemical bond breaking/forming …
A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method
PH König, M Hoffmann, T Frauenheim… - The Journal of Physical …, 2005 - ACS Publications
The performance of different link atom based frontier treatments in QM/MM simulations was
evaluated critically with SCC-DFTB as the QM method. In addition to the analysis of gas …
evaluated critically with SCC-DFTB as the QM method. In addition to the analysis of gas …
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
Y Zhang - Theoretical Chemistry Accounts, 2006 - Springer
This perspective article mainly focuses on the development and applications of a
pseudobond ab initio QM/MM approach to study enzyme reactions. The following aspects of …
pseudobond ab initio QM/MM approach to study enzyme reactions. The following aspects of …
Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase
We recently described a method to compute accurate quantum mechanical free energies
[Rod, TH; Ryde, U. Phys. Rev. Lett. 2005, 94, 138302]. The method, which we term quantum …
[Rod, TH; Ryde, U. Phys. Rev. Lett. 2005, 94, 138302]. The method, which we term quantum …