ProtCool 2.0: um gerador de protocolo para ancoragem e simulações de dinâmica molecular em complexos proteína-ligante em versão web
Abstract
The COVID-19 pandemic made evident the high demand for computational systems that speed up the indication of new drugs. In this sense, understanding the dynamic behavior of biomolecule complexes is essential However, the preparation of such simulations is highly complex, and their numerous details are not always sufficiently highlighted, compromising their reproducibility. Here, we propose the web tool ProtCool - a protocol generator, focused on the integration between docking and molecular dynamics of proteinligand complexes. Its use will be demonstrated in the simulation of the interaction between acetylcholinesterase and galantamine, used in the treatment of Alzheimer's.
References
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Guedes, F. C. (2021). ProtCool: um Gerador de Protocolos para Ancoragens e Simulações de Dinâmica Molecular em Complexos Proteína-Ligante. [Unifei]. [link].
Karplus, M. (2014). Development of multiscale models for complex chemical systems: From H+H2 to biomolecules (nobel lecture). Angewandte Chemie - International Edition, 53(38), 9992–10005. https://doi.org/10.1002/anie.201403924
McCammon, J. A., Gelin, B. R., & Karplus, M. (1977). Dynamics of folded protein. Nature, 267, 585–590. https://doi.org/10.1038/267585a0
Parks, J. M., Ph, D., Smith, J. C., & Ph, D. (2020). How to Discover Antiviral Drugs Quickly. The New England Journal of Medicine, 1–4. https://doi.org/10.1056/NEJMcibr2007042
Purawat, S., Ieong, P. U., Malmstrom, R. D., Chan, G. J., Yeung, A. K., Walker, R. C., Altintas, I., & Amaro, R. E. (2017). A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophysical Journal, 112(12), 2469–2474. https://doi.org/10.1016/j.bpj.2017.04.055
Ribeiro, J. V., Bernardi, R. C., Rudack, T., Stone, J. E., Phillips, J. C., Freddolino, P. L., & Schulten, K. (2016). QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts. Scientific Reports, 6(May), 1–14. https://doi.org/10.1038/srep26536
Rocha, R. E. O. (2017). Estudos de Modelagem Molecular dos Mecanismos de Afinidade Relativa para Quatro Galantamínicos com Potencial Anti-Alzheimer [UFMG]. [link].
Published
2023-06-27
How to Cite
SOUZA, Moisés P.; MAGNY, Levi M.; GUEDES, Fabiana C.; SILVEIRA, Carlos H. da.
ProtCool 2.0: um gerador de protocolo para ancoragem e simulações de dinâmica molecular em complexos proteína-ligante em versão web. In: TOOLS AND APPLICATIONS - BRAZILIAN SYMPOSIUM ON COMPUTING APPLIED TO HEALTHCARE (SBCAS), 23. , 2023, São Paulo/SP.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2023
.
p. 168-173.
ISSN 2763-8987.
DOI: https://doi.org/10.5753/sbcas_estendido.2023.231153.
