Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

Literature DB >> 26592101

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

Devleena Shivakumar¹, Edward Harder¹, Wolfgang Damm¹, Richard A Friesner², Woody Sherman¹.

Abstract

Explicit solvent molecular dynamics free energy perturbation simulations were performed to predict absolute solvation free energies of 239 diverse small molecules. We use OPLS2.0, the next generation OPLS force field, and compare the results with popular small molecule force fields-OPLS_2005, GAFF, and CHARMm-MSI. OPLS2.0 produces the best correlation with experimental data (R(2) = 0.95, slope = 0.96) and the lowest average unsigned errors (0.7 kcal/mol). Important classes of compounds that performed suboptimally with OPLS_2005 show significant improvements.

Year: 2012 PMID： 26592101 DOI： 10.1021/ct300203w

Source DB: PubMed Journal: J Chem Theory Comput ISSN： 1549-9618 Impact factor: 6.006

Keyword Cloud
Cited

56 in total

1. AB-Bind: Antibody binding mutational database for computational affinity predictions.

Authors: Sarah Sirin; James R Apgar; Eric M Bennett; Amy E Keating
Journal: Protein Sci Date: 2015-11-06 Impact factor: 6.725

2. Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

Authors: Caitlin C Bannan; Gaetano Calabró; Daisy Y Kyu; David L Mobley
Journal: J Chem Theory Comput Date: 2016-08-01 Impact factor: 6.006

3. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.

Authors: Daniel J Cole; Israel Cabeza de Vaca; William L Jorgensen
Journal: Medchemcomm Date: 2019-02-27 Impact factor: 3.597

Review 4. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors: A T Hagler
Journal: J Comput Aided Mol Des Date: 2018-11-30 Impact factor: 3.686

5. Assessing the performance of docking scoring function, FEP, MM-GBSA, and QM/MM-GBSA approaches on a series of PLK1 inhibitors.

Authors: Chunlan Pu; Guoyi Yan; Jianyou Shi; Rui Li
Journal: Medchemcomm Date: 2017-05-22 Impact factor: 3.597

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

1. AB-Bind: Antibody binding mutational database for computational affinity predictions.

2. Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

3. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.

Review 4. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

5. Assessing the performance of docking scoring function, FEP, MM-GBSA, and QM/MM-GBSA approaches on a series of PLK1 inhibitors.

6. Perspective: Alchemical free energy calculations for drug discovery.

7. Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

8. Determination of partial molar volumes from free energy perturbation theory.

9. Small Molecule Inhibitor that Stabilizes the Autoinhibited Conformation of the Oncogenic Tyrosine Phosphatase SHP2.

10. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.