Abstract: Fourteen scoring functions (Ligscore1, Ligscore2, Plp1, Plp2, Jain, Pmf, Ludi1, Ludi2, Ludi3, D-score, Pmf-score, G-score, Chemscore and Xscore) have been compared on a testing set containing 230 protein-ligand complexes to evaluate their abilities to reproduce experimentally determined structures and binding free energies after conformational sampling by the program Ligandfit. When applied to predict the binding free energy of the 230 protein-ligand complexes, Plp1, Plp2, G-score, Pmf and Xscore can give linear correlation coefficients over 0.50 between experimental determined and computed values. When employed to identify the experimentally observed conformation, if using root-mean-square deviation(rmsd)≤0.20 nm as the criterion, Ligscore1, Ligscore2, Plp1, Plp2 and Xscore can gain success rate larger than 70%. Combining any two or three of the 14 scoring functions into a consensus scoring function further improves the success rate to 80%. The results suggest that Xscore, plp1 and plp2 are more practicable than others in docking and scoring.

Key words: Binding free energy, Molecular docking, Scoring function, Consensus scoring function