ArticleJournal of molecular modeling2024
A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CB
Article in Journal of molecular modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Contact Occupancy and Per-Residue Energetic Contributions Distinguish Aflatoxin B1 Nanobodies with Different Binding Affinities.Biomolecules · 2026Article
- Review
- Moroccan virgin olive oil triterpenes: HPLC-DAD-ELSD profiling and computational investigation of anti-diabetic potential.BioImpacts : BI · 2026Article
- Exploring the inhibition mechanisms of momordin Ic on S. aureus serine/threonine phosphatase (Stp1) using theoretical and experimental approaches.Scientific reports · 2025Article
- Discovery of Novel DDR1 Inhibitors through a Hybrid Virtual Screening Pipeline, Biological Evaluation and Molecular Dynamics Simulations.ACS medicinal chemistry letters · 2025Article
- Structure-based molecular screening and dynamic simulation of phytocompounds targeting VEGFR-2: a novel therapeutic approach for papillary thyroid carcinoma.Frontiers in pharmacology · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
contextThe substantial increase in the number of active and inactive-state CB
methodsThe 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
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Registered trials
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