Simulasi Molecular Dynamics Protein-Ligand, Perhitungan MMPBSA Dan MMGBSA Menggunakan Gromacs

Authors

Purnawan Pontana Putra
Bioinformatics Research Center, INBIO Indonesia
Junaidin
Bioinformatics Research Center, INBIO Indonesia

Keywords:

Molecular Dynamics Protein Ligand, Simulasi, Protein, Ligand, Molecular, MMPBSA, MMGBSA, Gromacs

Synopsis

Molecular Dynamics (MD) sangat penting dalam kajian komputasi. Dengan GROMACS (GROningen MAchine for Chemical Simulations), peneliti dapat mensimulasikan Gerakan molekul protein-ligand dalam waktu tertentu dan mengamati bagaimana kompleks tersebut berinteraksi dalam kondisi yang lebih realistis karena memperhitungkan efek pelarut, pH, suhu clan tekanan.

Buku ini memuat dasar teori dan tutorial simulasi protein-ligand mulai dari tahap ionisasi, minimisasi, pemanasan, ekuilibrasi dan simulasi produksi menggunakan perangkat Lunak GROMACS. Di buku ini juga dibahas tutorial cara perhitungan free energy dengan pendekatan Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) dan Molecular Mechanics  Generalized Born Surface Area (MMGBSA)

Jumlah Halaman : 81

Ukuran Buku : A4

ISBN : 978-623-98383-3-1

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Simulasi Molecular Dynamics Protein-Ligand, Perhitungan MMPBSA Dan MMGBSA Menggunakan Gromacs

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1 May 2022

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