CHAPERONg Tutorials

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1. Protein in Water -- 1

Automated GROMACS MDS of ubiquitin in water. First time using CHAPERONg? Not very experienced with GROMACS itself? Start here!

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2. Protein in Water -- 2

Automated GROMACS MDS and trajectory analysis of the Kelch domain of the human KEAP1 in water. This is a more extended version of Tutorial 1.

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3. Protein-Ligand Compex in Water

Automated GROMACS MDS and trajectory analysis of the Kelch domain of the human KEAP1 complexed with an inhibitor.

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4. Umbrella Sampling 1: Protein-Ligand

Automated GROMACS enhanced (umbrella) sampling simulation of the Kelch domain of the human KEAP1 complexed with an inhibitor.

If you use CHAPERONg in your work please cite it as follows:

Yekeen A. A., Durojaye O. A., Idris M. O., Muritala H. F., & Arise R. O. (2023). CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses, Computational and Structural Biotechnology Journal 21: 4849-4858. [Link][PDF]

For BibTeX, you can insert the following:

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@article {yekeenCSBJ2023chaperong,
	author = {Abeeb Abiodun Yekeen and Olanrewaju Ayodeji Durojaye and Mukhtar Oluwaseun Idris and Hamdalat Folake Muritala and Rotimi Olusanya Arise},
	title = {{CHAPERONg}: A tool for automated {GROMACS}-based molecular dynamics simulations and trajectory analyses},
	journal = {{Computational and Structural Biotechnology Journal}},
	volume = {21},
	pages = {4849-4858},
	year = {2023},
	issn = {2001-0370},
	doi = {https://doi.org/10.1016/j.csbj.2023.09.024},
	publisher = {Elsevier},
	url = {https://www.sciencedirect.com/science/article/pii/S2001037023003367}
}