A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina

Abstract

Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock.

Enantioseparation of chiral pharmaceuticals by vancomycin‐bonded stationary phase and analysis of chiral recognition mechanism

“…29,30 In a molecular mechanics simulation, the primary mechanisms contained H-bonding, van der Waals interaction, steric repulsion, and electrostatic interaction. 29,30 In a molecular mechanics simulation, the primary mechanisms contained H-bonding, van der Waals interaction, steric repulsion, and electrostatic interaction.…”

“…It should be noticed that there were usually some assumptions in modeling chiral separations of chromatographic techniques using docking method, such as not taking solvation effect, buffer effect and entropy difference into consideration. org/) 29 and assumed as a macromolecular receptor. ncbi.nlm.nih.gov/).…”

Binding studies and biological evaluation of β-carotene as a potential inhibitor of human calcium/calmodulin-dependent protein kinase IV

“…Coordinates of both the protein and ligand (β-carotene) were prepared and subjected to docking using Autodock (version 4.2) [40,41]. The docked complex was further subjected to energy minimization, and final coordinates were used for structure analysis and binding energy prediction.…”

Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

“…Docking is also largely used for hit identification, representing the main example of receptor-based virtual screening (VS) procedure: a docking-based approach is commonly reported in several successful VS studies, both alone and in combination with other computational strategies [4][5][6][7][8] . For these reasons, the exponential attention that docking is gaining over time, as proved by the number of novel docking procedures and scoring functions reported in literature only in the last few years, cannot be blamed [9][10][11][12][13][14][15][16][17][18][19][20] . However, the remarkable interest for docking and for the development of new and optimized approaches is mainly due to the fact that the prediction of the actual binding mode of a ligand into a protein target is still far from being an easy task.…”