A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CB
Binding affinity
CB1 cannabinoid receptor
MM/GBSA
MM/PBSA
Molecular dynamics
Journal
Journal of molecular modeling
ISSN: 0948-5023
Titre abrégé: J Mol Model
Pays: Germany
ID NLM: 9806569
Informations de publication
Date de publication:
31 Oct 2024
31 Oct 2024
Historique:
received:
06
06
2024
accepted:
23
10
2024
medline:
1
11
2024
pubmed:
1
11
2024
entrez:
31
10
2024
Statut:
epublish
Résumé
The substantial increase in the number of active and inactive-state CB The study utilized the docked dataset (Induced Fit Docking with Glide XP scoring function) from Loo et al., consisting of 46 ligands-23 agonists and 23 antagonists. The equilibrated structures from Loo et al. were subjected to 30 ns production simulations using GROMACS 2018 at 300 K and 1 atm with the velocity rescaling thermostat and the Parinello-Rahman barostat. AMBER ff99SB*-ILDN was used for the proteins, General Amber Force Field (GAFF) was used for the ligands, and Slipids parameters were used for lipids. MM/PBSA and MM/GBSA binding free energies were then calculated using gmx_MMPBSA. The solute dielectric constant was varied between 1, 2, and 4 to study the effect of different solute dielectric constants on the performance of MM/PB(GB)SA. The effect of entropy on MM/PB(GB)SA binding free energies was evaluated using the interaction entropy module implemented in gmx_MMPBSA. Five GB models, GB
Identifiants
pubmed: 39480515
doi: 10.1007/s00894-024-06189-4
pii: 10.1007/s00894-024-06189-4
doi:
Substances chimiques
Receptor, Cannabinoid, CB1
0
Ligands
0
Cannabinoids
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
390Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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