Simulasi Molecular Dynamics Protein-Ligand, Perhitungan MMPBSA Dan MMGBSA Menggunakan Gromacs
Keywords:
Molecular Dynamics Protein Ligand, Simulasi, Protein, Ligand, Molecular, MMPBSA, MMGBSA, GromacsSynopsis
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
References
Hollingsworth SA, Dror RO, Physiology C, Engineering M. Molecular Dynemic Simulation for All. 2019;99(6):1129–43.
Spoel DVANDER, Lindahl E, Hess B, Groenhof G. GROMACS: Fast, Flexible, and Free. 2005;
D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, C. Jin, K. Ka and PAK. Amber 2021. Univ California, San Fr. 2021;
Attribution-sharealike CC, License I. AMBER Simulation Guide. 2020;
Coutsias EA, Wester MJ. RMSD and Symmetry. 2019;
Vassetti D, Pagliai M, Procacci P. Assessment of GAFF2 and OPLS-AA General Force Fields
in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy
of Druglike Organic Molecules. J Chem Theory Comput. 2019;15(3):1983–95.
Sousa Da Silva AW, Vranken WF. ACPYPE - AnteChamber PYthon Parser interfacE. BMC
Res Notes. 2012;5.
Valdés-Tresanco MS, Valdés-Tresanco ME, Valiente PA, Moreno E. gmx_MMPBSA Documentation [Internet]. 2021. Available from: https://valdes-tresanco- ms.github.io/gmx_MMPBSA/introduction/
Wang C, Greene D, Xiao L, Qi R, Luo R. Recent developments and applications of the
MMPBSA method. Front Mol Biosci. 2018;4(JAN).
Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding
affinities. Expert Opin Drug Discov. 2015;10(5):449–61.
Ali S, Hassan M, Islam A, Ahmad F. A Review of Methods Available to Estimate Solvent-
Accessible Surface Areas of Soluble Proteins in the Folded and Unfolded States. Curr Protein
Pept Sci. 2014;15(5):456–76.
Anwar N, Najam FA. Understanding Cross-Sections. Struct Cross Sect. 2017;39–136.
Hubbard RE, Kamran Haider M. Hydrogen Bonds in Proteins: Role and Strength. eLS. 2010;
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins Struct Funct Genet. 2006;65(3):712–25.
Lemkul JA. Pairwise-additive and polarizable atomistic force fields for molecular dynamics
simulations of proteins. Prog Mol Biol Transl Sci. 2020;170:1–71.
Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, et al. Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25.
Lemkul JA. GROMACS Tutorial Protein-Ligand Complex [Internet]. 2018. Available from: http://www.mdtutorials.com/gmx/complex/index.html
Junaidin J. Protokol Moleculer Dynamic Simulation Menggunakan Software GROMACS. Sekolah Tinggi Farmasi Muhammadiyah Tangerang; 2020. 26 p.
Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, Dror RO, et al. Improved side- chain torsion potentials for the Amber ff99SB protein force field. Proteins Struct Funct Bioinforma. 2010;78(8):1950–8.
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general Amber force field. J Comput Chem. 2004;25(9):1157–74.
Valdés-Tresanco MS, Valdés-Tresanco ME, Valiente PA, Moreno E. Gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). Gmx_MMPBSA: A New Tool to Perform End- State Free Energy Calculations with GROMACS. Journal of Chemic. J Chem Theory Comput. 2021;17(10):6281–91.
Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE. MMPBSA.py: An efficient program for end-state free energy calculations. J Chem Theory Comput. 2012;8(9):3314–21

