Validation of molecular force field parameters for peptides including isomerized amino acids

Chirality ◽  
2018 ◽  
Vol 30 (4) ◽  
pp. 332-341 ◽  
Author(s):  
Akifumi Oda ◽  
Tomoki Nakayoshi ◽  
Shuichi Fukuyoshi ◽  
Eiji Kurimoto ◽  
Noriyuki Yamaotsu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Molecular Force ◽  
Force Field Parameters ◽  
Molecular Force Field

Molecular force field evaluation by empirical constraints

1976 ◽  
Vol 73 ◽  
pp. 1051-1057
Author(s):  
Sadao Isotani ◽  
Alain J.-P. Alix
Keyword(s):  
Force Field ◽  
Field Evaluation ◽  
Molecular Force ◽  
Molecular Force Field

Molecular force field and structure of water: Recent microwave results

1974 ◽  
Vol 53 (1) ◽  
pp. 62-76 ◽  
Author(s):  
Robert L. Cook ◽  
Frank C. De Lucia ◽  
Paul Helminger
Keyword(s):  
Force Field ◽  
Structure Of Water ◽  
Molecular Force ◽  
Molecular Force Field

scholarly journals Pengaruh Minimisasi Energi MMFF94 dengan MarvinSketch dan Open Babel PyRx pada Penambatan Molekular Turunan Oksindola Tersubstitusi

ALCHEMY ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 33-40
Author(s):  
Atika Umi Hanif ◽  
Prima Agusti Lukis ◽  
Arif Fadlan
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Force Field ◽  
Binding Affinity ◽  
Energy Minimization ◽  
In Silico ◽  
Initial State ◽  
Molecular Force ◽  
Molecular Force Field ◽  
Docking Energy

 In silico technique is widely used for drug discovery because it can predict the conformation of ligands in protein macromolecules and it can calculate the binding affinity. The energy minimization is carried out to make the ligand more stable near the initial state during molecular docking process. The Merck Molecular Force Field (MMFF94) is one type of energy minimization process often used in organic compounds. The molecular docking of substituted oxindole derivatives on indoleamine macromolecules 2,3-dioxygenase (IDO-1, PDB: 2D0T) by MMFF94 minimization operated by MarvinSketch and Open Babel in PyRx showed different results. The binding affinity energy obtained was also quite different, but the ligands have the same conformation and bind the same residue with slightly different bond distances. Keywords: Molecular docking, energy minimization, substituted oxindole, Merck Molecular Force Field 94  Teknik in silico banyak digunakan untuk penemuan senyawa obat karena dapat memprediksi konformasi suatu ligan dalam makromolekul protein dan mampu menghitung nilai afinitas ikatan. Proses minimisasi energi dilakukan untuk menjadikan ligan lebih stabil mendekati keadaan awal selama penambatan molekular berlangsung. Merck Molecular Force Field (MMFF94) adalah salah satu jenis persamaan minimisasi energi yang sering digunakan pada senyawa organik. Hasil pengujian pengaruh minimisasi energi dengan MMFF94 menggunakan program MarvinSketch dan Open Babel dalam PyRx pada turunan oksindola tersubstitusi alkil terhadap makromolekul 2,3-dioxygenase indoleamine (IDO-1, PDB: 2D0T) menunjukkan hasil dengan nilai yang berbeda. Energi afinitas ikatan yang didapatkan juga cukup berbeda, namun ligan memiliki konformasi yang sama dan mengikat residu yang sama dengan jarak ikatan yang sedikit berbeda. Kata kunci: Penambatan molekular, minimisasi energi, oksindola tersubstitusi, Merck Molecular Force Field 94

Molecular Force Field of Methanol

1993 ◽  
Vol 26 (8) ◽  
pp. 1497-1510 ◽  
Author(s):  
Y. Hase ◽  
R. Forneris ◽  
S. C. da Silva
Keyword(s):  
Force Field ◽  
Molecular Force ◽  
Molecular Force Field
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