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Angewandte Chemie, ISSN 0044-8249, 07/2014, Volume 126, Issue 31, pp. 8345 - 8349
The retaining glycosyltransferase GalNAc‐T2 is a member of a large family of human polypeptide GalNAc‐transferases that is responsible for the... 
Röntgenbeugung | Acetamidogruppe | SNi‐Reaktionen | Proteine | QM/MM | Substrate Specificity | N-Acetylgalactosaminyltransferases - chemistry | Protein Conformation
Journal Article
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, ISSN 1463-9076, 07/2019, Volume 21, Issue 25, pp. 13578 - 13589
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 06/2013, Volume 135, Issue 24, pp. 8908 - 8919
Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have... 
DENSITY | ATP HYDROLYSIS | CARBONIC-ANHYDRASE | MOLECULAR-DYNAMICS | EG5 | FREE-ENERGY LANDSCAPES | MYOSIN | PROTON TRANSPORT | QM/MM | CHEMISTRY, MULTIDISCIPLINARY | INSIGHTS | Hydrolysis | Catalytic Domain | Adenosine Triphosphate - metabolism | Humans | Models, Molecular | Kinesin - chemistry | Kinesin - metabolism | Adenosine | Analysis | Chemical properties | Structure | Hydrogen bonding | Quantum theory
Journal Article
ACS Catalysis, ISSN 2155-5435, 12/2017, Volume 7, Issue 12, pp. 8130 - 8133
The retro-aldol reaction catalyzed by pyruvate class II aldolase is investigated with QM/MM metadynamics; this enzyme transforms the substrate of... 
metadynamics | salt bridge | QM/MM | aldolase | aldol cleavage | pyruvate | MECHANISM | CONVERGENT | CHEMISTRY, PHYSICAL
Journal Article
Chemistry – A European Journal, ISSN 0947-6539, 04/2018, Volume 24, Issue 20, p. n/a
Nature has evolved a unique covalent M‐Y‐W adduct in the active site of catalase−peroxidase (KatGs) to catalyze the decomposition of exessive hydrogen peroxide... 
metadynamics | KatG | QM/MM | catalase | PCET
Journal Article
Moscow University Chemistry Bulletin, ISSN 0027-1314, 7/2014, Volume 69, Issue 4, pp. 149 - 151
The mechanism of chemical transformations in the blue light photoreceptor domains (BLUF) implies the isomerization of the glutamine side chain. The Helmholtz... 
metadynamics | QM/MM method | Chemistry | BLUF domain | Chemistry/Food Science, general | Models | Isomerization | Quantum theory | Glutamine
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2010, Volume 6, Issue 4, pp. 1145 - 1156
The catalytic mechanism of Burkholderia cepacia lipase (BCL), which catalyzes the enantioselective hydrolysis of racemic esters of primary alcohols, was... 
Reaction Mechanisms | SERINE-PROTEASE CATALYSIS | ACTIVE-SITE | NUCLEAR-MAGNETIC-RESONANCE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | AB-INITIO QM/MM | TRANSITION-STATES | BARRIER HYDROGEN-BOND | MOLECULAR-DYNAMICS SIMULATION | SPACE GAUSSIAN PSEUDOPOTENTIALS | PSEUDOMONAS-CEPACIA | PRIMARY ALCOHOLS
Journal Article
ACS Catalysis, ISSN 2155-5435, 06/2015, Volume 5, Issue 6, pp. 3864 - 3875
Flap endonucleases (FENs) are nucleic acid hydrolyzing enzymes in charge of excising 5′-small DNA and RNA fragments (flaps) protruding from nucleic acid... 
metadynamics | catalytic mechanism | umbrella sampling | QM/MM | flap endonucleases | FALCIPAIN-2 INHIBITION | QUANTUM MECHANICS/MOLECULAR MECHANICS | AB-INITIO | CHEMISTRY, PHYSICAL | TRANSITION-STATES | FREE-ENERGY LANDSCAPES | METADYNAMICS SIMULATIONS | MOLECULAR-DYNAMICS SIMULATIONS | RIBONUCLEASE-H | BIOLOGICAL-SYSTEMS
Journal Article
ACTA NATURAE, ISSN 2075-8251, 10/2018, Volume 10, Issue 4, pp. 121 - 124
In this paper, we, for the first time, describe the interaction between the butyrylcholinesterase enzyme and echothiophate, a popular model compound and an... 
metadynamics | QM/MM | butyrylcholinesterase | organophosphates | echothiophate | CELL BIOLOGY
Journal Article
ACS Catalysis, ISSN 2155-5435, 2019, Volume 9, Issue 7, pp. 6276 - 6283
The transimination reaction involves conversion of an internal aldimine involving pyridoxal 5'-phosphate (PLP) and an enzyme to an external aldimine involving... 
metadynamics | temperature accelerated sliced sampling | QM/MM simulation | aspartate aminotransferase | transimination reaction | MOLECULAR-DYNAMICS | STATES | SPECIFICITY | CHEMISTRY, PHYSICAL | QM/MM | ENZYME | SCHIFF-BASES | 5-PHOSPHATE | SUBSTRATE
Journal Article
Chemistry - A European Journal, ISSN 0947-6539, 04/2018, Volume 24, Issue 20, pp. 5388 - 5395
Catalase-peroxidases (KatGs) are bifunctional enzymes exhibiting both peroxidase and substantial catalase activities. It is widely recognized from experiments... 
metadynamics | KatG | QM/MM | catalase | PCET | Protons | Catalytic Domain | Electron Transport | Oxidation-Reduction | Free Radicals - chemistry | Tryptophan - chemistry | Molecular Dynamics Simulation | Heme - chemistry | Methionine - chemistry | Peroxidases - chemistry | Oxygen - chemistry | Protein Conformation | Histidine - chemistry | Tyrosine - chemistry | Catalase - chemistry
Journal Article
Chemistry – A European Journal, ISSN 0947-6539, 04/2018, Volume 24, Issue 20, pp. 5388 - 5395
Catalase–peroxidases (KatGs) are bifunctional enzymes exhibiting both peroxidase and substantial catalase activities. It is widely recognized from experiments... 
metadynamics | KatG | QM/MM | catalase | PCET
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 06/2019, Volume 40, Issue 15, pp. 1538 - 1549
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2018, Volume 14, Issue 11, pp. 6093 - 6101
Drug–target binding kinetics has recently emerged as a sometimes critical determinant of in vivo efficacy and toxicity. Its rational optimization to improve... 
TRANSITION | METADYNAMICS | SMALL MOLECULES | FREE-ENERGY LANDSCAPE | SIDE-CHAIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | ABL | INHIBITOR | POLARIZATION | QM/MM SIMULATIONS | C-SRC | Binding | Polarization | State of the art | Computer simulation | Toxicity | Kinases | Free energy | Proteins | Side effects | Quantum mechanics | Ligands | Biocompatibility | In vivo methods and tests | Index Medicus
Journal Article
ACS Catalysis, ISSN 2155-5435, 01/2017, Volume 7, Issue 1, pp. 902 - 906
Employing hybrid quantum mechanics/molecular dynamics (QM/MM) molecular dynamics simulations and experimental mutational studies, we investigate the GTP... 
metadynamics | mutational studies | metaphosphate | iron transporter | proton transfer | QM/MM | substrate-assisted-catalysis | HAS-GTPase | ACTIVATION | RAS | CHEMISTRY, PHYSICAL | IRON ACQUISITION | MAJOR ROLE | GUANOSINE TRIPHOSPHATE | GAP PROTEIN COMPLEX | ELONGATION-FACTOR TU | SIMULATIONS | INSIGHTS
Journal Article
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