LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields
EG Kratz, AR Walker, L Lagardère… - Journal of …, 2016 - Wiley Online Library
We introduce an initial implementation of the LICHEM software package. LICHEM can
interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM …
interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM …
The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme
R Kaur, MM Aboelnga, DJ Nikkel… - Physical Chemistry …, 2022 - pubs.rsc.org
Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of
metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the …
metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the …
Calcium inhibition of ribonuclease H1 two-metal ion catalysis
Most phosphate-processing enzymes require Mg2+ as a cofactor to catalyze nucleotide
cleavage and transfer reactions. Ca2+ ions inhibit many of these enzymatic activities …
cleavage and transfer reactions. Ca2+ ions inhibit many of these enzymatic activities …
On the recognition of natural substrate CTP and endogenous inhibitor ddhCTP of SARS-CoV-2 RNA-dependent RNA polymerase: A molecular dynamics study
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 outbreak that is
affecting the entire planet. As the pandemic is still spreading worldwide, with multiple …
affecting the entire planet. As the pandemic is still spreading worldwide, with multiple …
[HTML][HTML] Theoretical study for determining the type of interactions between a GG block of an alginate chain with metals Cu2+, Mn2+, Ca2+ and Mg2+
CS Ardiles, CC Rodríguez - Arabian Journal of Chemistry, 2021 - Elsevier
The alginate interaction with divalent cations has been the subject of extensive study since
this biopolymer forms hydrogels in the presence of divalent cations (ionic crosslinking) …
this biopolymer forms hydrogels in the presence of divalent cations (ionic crosslinking) …
Toward a deeper understanding of enzyme reactions using the coupled ELF/NCI analysis: application to DNA repair enzymes
The combined Electron Localization Funtion (ELF)/Noncovalent Interaction (NCI) topological
analysis (Gillet et al. J. Chem. Theory Comput. 2012, 8, 3993) has been extended to …
analysis (Gillet et al. J. Chem. Theory Comput. 2012, 8, 3993) has been extended to …
The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
J Sgrignani, A Magistrato - The Journal of Physical Chemistry B, 2012 - ACS Publications
According to the RNA world hypothesis, self-replicating ribozymes, storing the genetic
information and being able to perform catalysis, were the constituents of the first living …
information and being able to perform catalysis, were the constituents of the first living …
Computational simulations of DNA polymerases: detailed insights on structure/function/mechanism from native proteins to cancer variants
AR Walker, GA Cisneros - Chemical research in toxicology, 2017 - ACS Publications
Genetic information is vital in the cell cycle of DNA-based organisms. DNA polymerases
(DNA Pols) are crucial players in transactions dealing with these processes. Therefore, the …
(DNA Pols) are crucial players in transactions dealing with these processes. Therefore, the …
Combining evolutionary conservation and quantum topological analyses to determine quantum mechanics subsystems for biomolecular quantum mechanics …
Selection of residues and other molecular fragments for inclusion in the quantum mechanics
(QM) region for QM/molecular mechanics (MM) simulations is an important step for these …
(QM) region for QM/molecular mechanics (MM) simulations is an important step for these …
Joint Use of bonding evolution theory and QM/MM hybrid method for understanding the hydrogen abstraction mechanism via cytochrome P450 aromatase
I Viciano, P Gonzalez-Navarrete… - Journal of Chemical …, 2015 - ACS Publications
Bonding evolution theory (BET), as a combination of the electron localization function (ELF)
and Thom's catastrophe theory (CT), has been coupled with quantum mechanics/molecular …
and Thom's catastrophe theory (CT), has been coupled with quantum mechanics/molecular …