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searching for QM/MM 39 found (73 total)

alternate case: qM/MM

CP2K (582 words) [view diff] exact match in snippet view article find links to article

tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential

Comparison of software for molecular mechanics modeling (379 words) [view diff] no match in snippet view article find links to article

Molecule ADF Yes Yes Yes Yes Yes No Yes Yes Yes Modeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational

Mozenavir (265 words) [view diff] exact match in snippet view article find links to article

Hermann JC, Nam K, Ma S, Gao J, Höltje HD (December 2004). "A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1

Plastocyanin (1,690 words) [view diff] exact match in snippet view article find links to article

plastocyanin, methods such as quantum mechanics / molecular mechanics (QM/MM) molecular dynamics simulations. This method was used to determine that

Lysozyme (4,285 words) [view diff] exact match in snippet view article find links to article

proposed by Koshland. More recently, quantum mechanics/ molecular mechanics (QM/MM) molecular dynamics simulations have been using the crystal of HEWL and

Kenneth M. Merz Jr. (1,427 words) [view diff] exact match in snippet view article find links to article

linear-scaling quantum mechanical methods in biological and pharmaceutical sciences; QM/MM methods; force field design for proteins and metalloenzymes; atomic point

Oxygen-evolving complex (503 words) [view diff] exact match in snippet view article find links to article

Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray

Mechanism of action (1,851 words) [view diff] exact match in snippet view article find links to article

irreversible inhibition of human cyclooxygenase-1 by aspirin as predicted by QM/MM calculations". Journal of Molecular Graphics and Modelling. 40: 99–109.

Lethal synthesis (393 words) [view diff] exact match in snippet view article find links to article

""Lethal Synthesis" of Fluorocitrate by Citrate Synthase Explained through QM/MM Modeling". Angewandte Chemie International Edition. 50 (44): 10349–10351

Thermodynamic integration (802 words) [view diff] exact match in snippet view article find links to article

Algorithms to Applications. Academic Press, 2007 J Kästner; et al. (2006). "QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella

List of quantum chemistry and solid-state physics software (510 words) [view diff] exact match in snippet view article find links to article

spectrum and seamless (HF, MCSCF, GVB, MP2, DFT, TDDFT, CHARMM, AMBER, OPLSAA) QM/MM package integrated in GAMESS-US. 10 Through CRYSCOR Archived 2019-12-26

Aspartoacylase (1,649 words) [view diff] exact match in snippet view article find links to article

acid–general base reaction mechanism for human brain aspartoacylase: A QM/MM study". Computational and Theoretical Chemistry. 980: 85–91. doi:10.1016/j

Muconate lactonizing enzyme (2,057 words) [view diff] exact match in snippet view article find links to article

favorable portions according to Quantum Mechanics/Molecular Mechanics (QM/MM) analysis. The second strand of the MLE contains a basic residue that allows

Macrophomic acid (540 words) [view diff] exact match in snippet view article find links to article

This pathway is thought to be the actual mechanism; however, according to QM/MM calculations, it seems that the Michael-aldol sequence is more energetically

Swainsonine (1,801 words) [view diff] exact match in snippet view article find links to article

Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation". Journal of the American Chemical Society. 132

PQS (software) (1,465 words) [view diff] exact match in snippet view article

parametrized. Molecular Mechanics using the Sybyl 5.2 and UFF Force Fields. QM/MM using the ONIOM method. Molecular dynamics using the simple Verlet algorithm

List of computational chemists (1,018 words) [view diff] exact match in snippet view article find links to article

Molecular Dynamics and Chemoinformatics Ursula Rothlisberger, developer of QM/MM methods Kenneth Ruud (1969–), developer of Dalton Yousef Saad, developer

Mechanism of action of aspirin (1,734 words) [view diff] exact match in snippet view article find links to article

irreversible inhibition of human cyclooxygenase-1 by aspirin as predicted by QM/MM calculations". Journal of Molecular Graphics & Modelling. 40: 99–109. doi:10

Serine hydroxymethyltransferase (2,378 words) [view diff] exact match in snippet view article find links to article

Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study". ACS Catalysis. 8 (11): 10096–10110. doi:10.1021/acscatal.8b02321

VOTCA (519 words) [view diff] exact match in snippet view article find links to article

and a basic DFT implementation, employing localized basissets. Polarized QM/MM calculations for excited states are provided in the Thole framework. It

Lactoylglutathione lyase (4,553 words) [view diff] exact match in snippet view article find links to article

by density functional theory, molecular dynamics simulations and hybrid QM/MM methods. The reason for the special specificity of the enzyme (it accepts

Clémence Corminboeuf (903 words) [view diff] exact match in snippet view article find links to article

"Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein". Journal of the American Chemical

Dynemicin A (1,155 words) [view diff] exact match in snippet view article find links to article

PMID 15984874. Tuttle, Tell; Kraka, Elfi; Theil, Walter; Cremer, Dieter (2007). "A QM/MM Study of the Bergman Reaction of Dynemicin A in the Minor Groove of DNA"

MMP3 (3,031 words) [view diff] exact match in snippet view article find links to article

2015). "Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling". Journal of Computational Chemistry. 36 (21): 1621–30. doi:10

Fluorinase (1,029 words) [view diff] exact match in snippet view article find links to article

(October 2005). "Insight into enzymatic C-F bond formation from QM and QM/MM calculations". Journal of the American Chemical Society. 127 (39): 13643–55

Alpha-methylacyl-CoA racemase (2,219 words) [view diff] exact match in snippet view article find links to article

structure of a reaction intermediate complex characterized by detailed QM/MM calculations". The Journal of Physical Chemistry B. 116 (11): 3619–29. doi:10

Force field (chemistry) (9,838 words) [view diff] exact match in snippet view article

widely used for both small molecules and macromolecules COSMOS-NMR – hybrid QM/MM force field adapted to various inorganic compounds, organic compounds, and

Paraoxonase (1,706 words) [view diff] exact match in snippet view article find links to article

Paraoxonase 1 (PON1): Experimental and Quantum Mechanics/Molecular Mechanics (QM/MM) Studies." The Journal of Physical Chemistry B 119.30 (2015):9571-9585.

Arginine finger (1,644 words) [view diff] exact match in snippet view article find links to article

Jürgen (2007-12-11). "Role of the arginine finger in Ras·RasGAP revealed by QM/MM calculations". FEBS Letters. 581 (29): 5677–5684. doi:10.1016/j.febslet

Sam Hay (chemist) (922 words) [view diff] exact match in snippet view article

Greenwich from 2019 - 2022. Hay was also the co-organiser of the MGMS ‘QM/MM methods and applications’ conference held in 2017. In 2012, Hay and Nigel

Enzyme inhibitor (11,575 words) [view diff] exact match in snippet view article find links to article

(March 2021). "Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies". International Journal of Molecular Sciences. 22 (6): 3232. doi:10

Isethionate sulfite-lyase (1,055 words) [view diff] exact match in snippet view article find links to article

(December 2021). "Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations". Journal of Chemical Information and Modeling. 61 (12): 5871–5882

Limonene-1,2-epoxide hydrolase (1,342 words) [view diff] exact match in snippet view article find links to article

PMID 10329649. Hou QQ, Sheng X, Wang JH, Liu YJ, Liu CB (February 2012). "QM/MM study of the mechanism of enzymatic limonene 1,2-epoxide hydrolysis". Biochimica

Urey–Bigeleisen–Mayer equation (2,369 words) [view diff] exact match in snippet view article find links to article

PMID 25936775. Giese, T.J.; Zeng, J.; Ekesan, S.; York, D.M. (2022). "Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles

Spirotetronate cyclase AbyU (1,045 words) [view diff] exact match in snippet view article find links to article

Diels-Alder mechanism as indicated by Quantum mechanics/molecular mechanics (QM/MM) MD simulations. Higher-level density functional theory calculations support

Interatomic potential (7,343 words) [view diff] exact match in snippet view article find links to article

Jorgensen WL (January 2010). "Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions". Accounts of Chemical

Serena DeBeer (2,544 words) [view diff] exact match in snippet view article find links to article

structure of the E 1 state of Mo nitrogenase through Mo and Fe K-edge EXAFS and QM/MM calculations". Chemical Science. 10 (42): 9807–9821. doi:10.1039/C9SC02187F

Biodesulfurization (3,424 words) [view diff] exact match in snippet view article find links to article

2016). "Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)"

Lysine acetylsalicylate (2,793 words) [view diff] exact match in snippet view article find links to article

irreversible inhibition of human cyclooxygenase-1 by aspirin as predicted by QM/MM calculations". Journal of Molecular Graphics & Modelling. 40: 99–109. doi:10