HeroMDAnalysis: An Automagical Tool for GROMACS-Based Molecular Dynamics Simulation Analysis

Rawat, Ravi; Kant, Kamal; Kumar, Anoop; Bhati, Kajal; Verma, Saurabh

doi:10.4155/fmc-2020-0191

Cited by 58 publications

(15 citation statements)

References 10 publications

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“…72 The molecular dynamics simulation study was performed for a 10 ns time period at 300 K temperature and 1 bar pressure using the GROMACS 2020.1 simulation package, and the resulting data was analyzed. 73,74 5.4.4. In Silico Prediction of ADMET Parameters.…”

Section: Chemistry 521 Synthesis Of Substituted Isatinsmentioning

confidence: 99%

“…Taking the NPT ensemble, the final production MD simulation was carried out, and the long-range electrostatic interactions were identified by using the particle mesh Ewald (PME) method . The molecular dynamics simulation study was performed for a 10 ns time period at 300 K temperature and 1 bar pressure using the GROMACS 2020.1 simulation package, and the resulting data was analyzed. , …”

Section: Experimental Sectionmentioning

confidence: 99%

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Further Studies on Triazinoindoles as Potential Novel Multitarget-Directed Anti-Alzheimer’s Agents

Patel

Kanhed

et al. 2020

ACS Chem. Neurosci.

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The inadequate clinical efficacy of the present anti-Alzheimer’s disease (AD) drugs and their low impact on the progression of Alzheimer’s disease in patients have revised the research focus from single targets to multitarget-directed ligands. A novel series of substituted triazinoindole derivatives were obtained by introducing various substituents on the indole ring for the development of multitarget-directed ligands as anti-AD agents. The experimental data indicated that some of these compounds exhibited significant anti-AD properties. Among them, 8-(piperidin-1-yl)-N-(6-(pyrrolidin-1-yl)hexyl)-5H-[1,2,4]triazino[5,6-b]indol-3-amine (60), the most potent cholinesterase inhibitor (AChE, IC50 value of 0.32 μM; BuChE, IC50 value of 0.21 μM), was also found to possess significant self-mediated Aβ1–42 aggregation inhibitory activity (54% at 25 μM concentration). Additionally, compound 60 showed strong antioxidant activity. In the PAMPA assay, compound 60 exhibited blood-brain barrier penetrating ability. An acute toxicity study in rats demonstrated no sign of toxicity at doses up to 2000 mg/kg. Furthermore, compound 60 significantly restored the cognitive deficits in the scopolamine-induced mice model and Aβ1–42-induced rat model. In the in silico ADMET prediction studies, the compound satisfied all the parameters of CNS acting drugs. These results highlighted the potential of compound 60 to be a promising multitarget-directed ligand for the development of potential anti-AD drugs.

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Section: Chemistry 521 Synthesis Of Substituted Isatinsmentioning

confidence: 99%

Section: Experimental Sectionmentioning

confidence: 99%

Further Studies on Triazinoindoles as Potential Novel Multitarget-Directed Anti-Alzheimer’s Agents

Patel

Kanhed

et al. 2020

ACS Chem. Neurosci.

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“…Recently, many computer-based simulation tools have been used in molecular biology. For example, GROMACS, an automated tool, has been applied for molecular dynamics (MD) simulation of the ligand–protein complex …”

Section: Introductionmentioning

confidence: 99%

“…For example, GROMACS, an automated tool, has been applied for molecular dynamics (MD) simulation of the ligand−protein complex. 13 The MD simulation is a powerful method to understand the macroscopic properties of systems at the molecular and atomic levels in time and space. It has been used to investigate channel−molecule interactions.…”

Section: Introductionmentioning

confidence: 99%

ATP-Binding Cassette Exporter PDR11-Mediated Terpenoid Secretion in Engineered Yeast

Han

Yang

et al. 2023

ACS Synth. Biol.

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The metabolic burden caused by terpenoid accumulation limits the development of highly efficient microbial cell factories, which can be circumvented using exporter-mediated product secretion. Although our previous study showed that the pleiotropic drug resistance exporter (PDR11) mediates the export of rubusoside in Saccharomyces cerevisiae, the underlying mechanism is still unclear. Herein, we used GROMACS software to simulate PDR11-mediated rubusoside recruitment and found six residues (D116, D167, Y168, P521, R663, and L1146) on PDR11 that are critical for this process. We also explored the exportation potential of PDR11 for 39 terpenoids by calculating their binding affinity using batch molecular docking. Then, we verified the accuracy of the predicted results by conducting experiments with squalene, lycopene, and β-carotene as examples. We found that PDR11 can efficiently secrete terpenoids with binding affinities lower than −9.0 kcal/mol. Combining the computer-based prediction and experimental verification, we proved that binding affinity is a reliable parameter to screen exporter substrates and might potentially enable rapid screening of exporters for natural products in microbial cell factories.

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“…In contrast, the HeroMDAnalysis tool allows for the generation of different plots in high-definition quality images. However, it does not produce an output report file where all results are orderly structured 8 . Besides obtaining a report file with all the data neatly organized, ASGARD allows access to all the raw data and plot files generated by the analysis workflow like the compared tools.…”

mentioning

confidence: 99%

ASGARD. A simple and automatic GROMACS tool to analyze Molecular Dynamic simulations

Rodriguez-Martínez

Nelen

Carmena-Bargueño

et al. 2023

Preprint

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One of the most featured techniques to analyze the physical movement of molecules is Molecular Dynamics (MD) simulations. Among the different programs used to perform them, GROMACS is one of the most widely used open-source packages. We present ASGARD, a software to perform analysis of MD protein or protein-ligand complex simulations and to generate the corresponding report via an automated MD workflow. This tool automatically generates a set of analyses after completing the simulation, including reports about overall system stability and system flexibility analysis with RMSD Fluctuation and Distribution calculations. Finally, a dynamic analysis with SASA and DSSP method graphs, and different interaction analyses are performed. In conclusion, ASGARD allows the user to run MD simulation analysis with a single command line instead of using the GROMACS programs individually. Following this, it automatically creates an analysis report which helps to understand the molecular interactions and structural changes.

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HeroMDAnalysis: An Automagical Tool for GROMACS-Based Molecular Dynamics Simulation Analysis

Cited by 58 publications

References 10 publications

Further Studies on Triazinoindoles as Potential Novel Multitarget-Directed Anti-Alzheimer’s Agents

Further Studies on Triazinoindoles as Potential Novel Multitarget-Directed Anti-Alzheimer’s Agents

ATP-Binding Cassette Exporter PDR11-Mediated Terpenoid Secretion in Engineered Yeast

ASGARD. A simple and automatic GROMACS tool to analyze Molecular Dynamic simulations

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