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International Journal of Zoology and Applied Biosciences Research Article

RMSD-Based molecular dynamics investigation of parkinson’s disease therapeutic targets using gromacs

Vinothini, Lourdu Brissilla Mary Varghese, Devasena B, Kaaviya A A and Jenifer E

Year : 2025 | Pages: 443-446

doi: https://doi.org/10.55126/ijzab.2025.v10.i06.SP088

Received on: 25/09/2025

Revised on: 23/10/2025

Accepted on: 22/11/2025

Published on: 01/12/2025

  • Vinothini, Lourdu Brissilla Mary Varghese, Devasena B, Kaaviya A A and Jenifer E ( 2025).

    RMSD-Based molecular dynamics investigation of parkinson’s disease therapeutic targets using gromacs

    . International Journal of Zoology and Applied Biosciences, 10( 6), 443-446.

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Abstract

Understanding conformational stability and structural deviations of Parkinson’s disease (PD)–related proteins is essential for rational drug design. We performed atomistic molecular dynamics (MD) simulations using GROMACS to investigate the conformational dynamics of two therapeutically relevant PD proteins ?-synuclein and the kinase domain of LRRK2. Simulations (200 ns × triplicate for each system) were analyzed by root-mean-square deviation (RMSD) and complementary metrics (RMSF, radius of gyration, secondary structure evolution). RMSD trajectories revealed distinct stability profiles: LRRK2 kinase domain stabilized within ~20-50 ns showing RMSD plateaus ~1.5–2.5 Å, while ?-synuclein showed higher RMSD fluctuations consistent with its intrinsically disordered nature. These results provide structural insight into dynamic regions that could be targeted in drug discovery pipelines. The manuscript includes full methods, sample GROMACS commands, and recommendations for reproducible RMSD analyses in PD protein MD studies.

Keywords

Medicinal plants, Hepatocellular carcinoma, Liver cancer, Anticancer activity, Phytochemicals.

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    © The Author(s) 2025. This article is published by International Journal of Zoology and Applied Biosciences under the terms of the Creative Commons Attribution 4.0 International License (creativecommons.org), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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