LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

Dodda, Leela S.; Vaca, Israel Cabeza de; Tirado‐Rives, Julian; Jorgensen, William L.

doi:10.1093/nar/gkx312

Cited by 942 publications

(675 citation statements)

References 43 publications

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“…All bonded and LJ interaction parameters were compiled from the LigParGen Server. 62,63 We utilized the LAMMPS software package for all MD simulations. 64 Forces and positions were evaluated every 1.0 fs at 600 K and 1.0 atm (Nosé-Hoover thermostat, Parinello-Rahman barostat), with LJ and Coulombic pair energies evaluated using eq.…”

Section: Simulation and Analysis Methodsologymentioning

confidence: 99%

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Ion transport mechanisms in salt‐doped polymerized zwitterionic electrolytes

Keith

Ganesan

2020

Journal of Polymer Science

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Polyzwitterions (polyZIs), macromolecules with repeating ampholytic monomers, are a novel class of materials with attractive properties for battery electrolytes. In this study, we probe the ion transport characteristics and underlying mechanisms in two salt‐doped (Li+‐TFSI−) polyZIs of similar composition with contrasting zwitterion (ZI) ionic organization: pendant monomers organized via backbone‐anion‐cation (B‐ZI−‐ZI+, Motif B) and backbone‐cation‐anion (B‐ZI+‐ZI−, Motif C). Within both Motifs B and C, the counterion of the pendant‐end ZI moiety shows higher mobility. Similarly, when comparing Li+ or TFSI− across motifs, it is seen that the respective pendant‐end counterion possesses higher mobility than its backbone‐adjacent counterpart. Furthermore, when comparing counterions to same‐position ZI moieties, TFSI− is seen to possess higher mobility than Li+ in each case, a result rationalized by invoking the lower interaction strength between the TFSI− and ZI+. Analysis of ion‐transport mechanisms demonstrate that the mobility of countercharges to the pendant‐end ZI moiety correlates with the ion‐association relaxation timescale, similar to ideas noted in polymerized ionic liquids in past studies. However, the mobility of countercharges to the backbone‐adjacent ZI moiety is shown to be correlated with a cage relaxation time, which incorporates the combined effects of frustrated motion due to the presence of the polymer backbone and pendant‐end ZI moiety and the higher mobility in a population of lightly ZI‐coordinated ions. © 2020 Wiley Periodicals, Inc. J. Polym. Sci. 2020, 58, 578–588

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Section: Simulation and Analysis Methodsologymentioning

confidence: 99%

“…Simulation boxes were packed with polymers of Motifs B or C, along with Li + ‐TFSI − salt in systematically varied fractions relative to polyZI monomers ( r mol salt /mol ZI ). All bonded and LJ interaction parameters were compiled from the LigParGen Server . We utilized the LAMMPS software package for all MD simulations .…”

Section: Introductionmentioning

confidence: 99%

Ion transport mechanisms in salt‐doped polymerized zwitterionic electrolytes

Keith

Ganesan

2020

Journal of Polymer Science

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“…Molecular dynamics (MD) simulations : LigParGen webserver was used to generate topology and parameter files of the NSC76027 optimized structure (NSC76027 input files). All‐atom MD simulations were performed using the NAMD simulation package for EctopoIcc alone and the ternary complex.…”

Section: Methodsmentioning

confidence: 99%

Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development

et al. 2020

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A topoisomerase‐DNA transient covalent complex can be a druggable target for novel topoisomerase poison inhibitors that represent a new class of antibacterial or anticancer drugs. Herein, we have investigated molecular features of the functionally important Escherichia coli topoisomerase I (EctopoI)‐DNA covalent complex (EctopoIcc) for molecular simulations, which is very useful in the development of new antibacterial drugs. To demonstrate the usefulness of our approach, we used a model small molecule (SM), NSC76027, obtained from virtual screening. We examined the direct binding of NSC76027 to EctopoI as well as inhibition of EctopoI relaxation activity of this SM via experimental techniques. We then performed molecular dynamics (MD) simulations to investigate the dynamics and stability of EctopoIcc and EctopoI‐NSC76027‐DNA ternary complex. Our simulation results show that NSC76027 forms a stable ternary complex with EctopoIcc. EctopoI investigated here also serves as a model system for investigating a complex of topoisomerase and DNA in which DNA is covalently attached to the protein.

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“…To enumerate the thermodynamic behavior of histone methyltransferase and elucidate the mechanism of its inhibition, MDS was carried out in the combinations of protein alone and protein complexes with ligand, H3K4 peptide and H3K9 peptide. The topology of protein was created using the OPLSA program and ligand topology parameterization was created using LigParGen [30] an OPLS-AA parameterization server for organic ligands.…”

Section: Molecular Dynamics (Md) Simulationsmentioning

confidence: 99%

Discovery of potential epigenetic inhibitors against histone methyltransferases through molecular docking and molecular dynamics simulations

Babu

Zhang

Qin

et al. 2020

Preprint

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Histone methyltransferases (HMTases) catalyze histone methylations that are the important epigenetic marks regulating gene expression, cell fate, and disease progression. In this study, we investigated potential epigenetic inhibitors against HMTases through in silico approaches, including ensembled molecular docking and molecular dynamics simulations (MDS).We identified three candidate compounds, including echinomycin, emetine, and streptonigrin, which showed interactions with HMTases. Echinomycin showed similar binding affinity with H3K4-HMTase NSD3 and H3K9-HMTase SETDB1 but streptonigrin and emetine had preferential binding affinity with NSD3 and SETDB1, respectively. The binding of NSD3 to streptonigrin and echinomycin and binding of SETDB1 to emetine and echinomycin were further confirmed by the results of hydrogen bonding profile and MM/PBSA calculations. Together, our results uncover the binding affinities of echinomycin, emetine, and streptonigrin with histone methyltransferases, and suggest that these compounds are potential epigenetic inhibitors regulating cell activities.

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LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

Cited by 942 publications

References 43 publications

Ion transport mechanisms in salt‐doped polymerized zwitterionic electrolytes

Ion transport mechanisms in salt‐doped polymerized zwitterionic electrolytes

Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development

Discovery of potential epigenetic inhibitors against histone methyltransferases through molecular docking and molecular dynamics simulations

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