Pose Prediction

Figure 2.126. (fred cdk2) The crystallographic structure of a CDK-2 ligand in its bound conformation (green) overlaid by the pose predicted by FRED... 

McGann M (2011) FRED pose prediction and virtual screening accuracy. J Chem Inf Model 51 578-596... 

H. Chen, P. D. Lyne, F. Giordanetto, T. Lovell and J. Li, On evaluating molecular-docking methods for pose prediction and enrichment factors., J. Chem. Inf. Model., 2006, 46, 401 15. 

Ligand Binding Pose Prediction with the Flexible Pocketome... 

Fig. 8. The accuracy of the ligand binding pose prediction for different ensemble sizes. The tors reflect the fraction of the ligands that dock correctly using traditional ensemble docking and 4D docking for varying ensemble size, compared to the accuracy of a single-receptor cross-docking.

There are several approaches to address the issue of scoring and to improve the performance of scoring functions in terms of pose prediction and affinity correlation. A selection of recent developments is discussed in the next section. 

Jain, A.N. (2009) Fffects of protein conformation in docking improved pose prediction through protein pocket adaptation. Journal of Computer-Aided Molecular Design, 23 (6), 355-374. 

Cross, J., Thompson, D., Rai, B., Baber, C., Fan, K., Hu, Y and Humblet, C. (2009) Comparison of several molecular docking programs pose prediction and virtual screening accuracy. Journal of Chemical Information and Modeling, 49, 1455-1474. 

Active Site-Directed Pose Prediction Programs for Efficient Filtering of Molecules... 

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