MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27018
Abstract: We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and… read more here.
Keywords: mechanics molecular; setup quantum; quantum mechanics; toolkit setup ... See more keywords
Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations.
Sign Up to like & getrecommendations! Published in 2021 at "Archives of biochemistry and biophysics"
DOI: 10.1016/j.abb.2021.108807
Abstract: The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with… read more here.
Keywords: biosynthesis; hybrid quantum; molecular mechanics; mechanics molecular ... See more keywords
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00057
Abstract: FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants… read more here.
Keywords: novel esterase; mechanics molecular; molecular mechanics; fmta ... See more keywords
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c01505
Abstract: We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK… read more here.
Keywords: mechanics molecular; molecular mechanics; quantum mechanics; graphics processing ... See more keywords
Vertical Excitation Energies and Lifetimes of the Two Lowest Singlet Excited States of Cytosine, 5-Aza-cytosine, and the Triazine Family: Quantum Mechanics–Molecular Mechanics Studies
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c01262
Abstract: A swarm of semi-classical quantum mechanics/molecular mechanics molecular-dynamics simulations where OM2/MNDO is combined with the Gromacs program for consideration of explicit water is performed, solving the time-dependent Schrödinger equation in each step of the trajectories… read more here.
Keywords: mechanics molecular; molecular mechanics; triazine; quantum mechanics ... See more keywords
Structure and Dynamics of the Reactive State for the Histidine Methylation Process and Catalytic Mechanism of SETD3: Insights from Quantum Mechanics/Molecular Mechanics Investigation
Sign Up to like & getrecommendations! Published in 2020 at "ACS Catalysis"
DOI: 10.1021/acscatal.0c03390
Abstract: The SETD3 enzyme adds a methyl group to Ne2 of His73 in β-actin, and such methylation finetunes actin’s biochemical properties and cellular function. Here, quantum mechanics/molecular mechanics mol... read more here.
Keywords: methylation; molecular mechanics; mechanics molecular; setd3 ... See more keywords
Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B
Sign Up to like & getrecommendations! Published in 2017 at "ACS Catalysis"
DOI: 10.1021/acscatal.6b02310
Abstract: Classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the origin of the enantioselectivity of the Candida antarctica lipase B (CalB) catalyzed O-acetylation of (R,S)-propranolol. The reaction is… read more here.
Keywords: candida antarctica; molecular mechanics; mechanics molecular; quantum mechanics ... See more keywords
Combined quantum mechanics/molecular mechanics (QM/MM) methods to understand the charge density distribution of estrogens in the active site of estrogen receptors
Sign Up to like & getrecommendations! Published in 2019 at "RSC Advances"
DOI: 10.1039/c9ra08607b
Abstract: The ligand binding to protein and host–guest interactions are ubiquitous for molecular recognition. read more here.
Keywords: molecular mechanics; mechanics molecular; quantum mechanics; mechanics methods ... See more keywords
Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin
Sign Up to like & getrecommendations! Published in 2017 at "Chinese Journal of Chemical Physics"
DOI: 10.1063/1674-0068/30/cjcp1709169
Abstract: Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B1 and B2 states) of myoglobin… read more here.
Keywords: mechanics molecular; distal pocket; heme distal; initio quantum ... See more keywords
Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Biomolecular Structure and Dynamics"
DOI: 10.1080/07391102.2019.1574605
Abstract: Abstract The resistance to the endocrine therapy of breast cancer leads to the emergence of new class of drugs that downregulates the estrogen receptor action known as selective estrogen receptor downregulators (SERDs). The first approved… read more here.
Keywords: molecule; bri molecule; mechanics molecular; estrogen receptor ... See more keywords
Identification of novel flavonoid inhibitor of Catechol-O-Methyltransferase enzyme by molecular screening, quantum mechanics/molecular mechanics and molecular dynamics simulations
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Biomolecular Structure and Dynamics"
DOI: 10.1080/07391102.2019.1699446
Abstract: Abstract The low level of dopamine at substantia nigra (mid-brain) has been considered to be one of the reasons for Parkinson’s disease (PD). This dopamine deficit is due to the influence of Catechol-O-Methyltransferase (COMT). A… read more here.
Keywords: molecular screening; comt enzyme; molecular dynamics; mechanics molecular ... See more keywords