Docking methods assessment

Virtual screening uses computational docking methods to assess which of a large database of compounds will fit into the unliganded structure of the target protein. Current protocols and methods can, with up to 80% success, predict the binding position and orientation of ligands that are known to bind... 

Structures of protein complexes are the basis for understanding protein interactions. Many of fhese structures will have to be built by docking. CAPRI provides a forum for crifical assessment of docking methods. Methods making use of experimental or predicted interface information appear promising. 

Fully flexible docking methods are a step toward more reliable compound assessment. For their application in structure-based virtual screening, some effects... 

R. Mendez, R. Leplae, L. De Maria, and S. J. Wodak, Proteins, 52, 51-67 (2003). Assessment of Blind Predictions of Protein-Protein Interactions Current Status of Docking Methods. 

Eriesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Erancis P, Shenkin PS. Glide a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004 47 1739-49. 

Glide a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7) 1739-1749. 

The binding energy (AEh) of the docked CDNB used to assess the relative affinities of the docked ligand at the H-site of the different GST-pi variants was calculated using the CFF91 force field, according to the method of Robinson et al.31 as shown in Equation 15.2 ... 

R A Friesner, J L Banks, R B Murphy, T A Halgren, J J Klicic, D T Mainz, M P Repasky, E H Knoll, M Shelley, J K Perry, D E Shaw, P Francis, P S Shenkin (2004) Glide A New Approach for Rapid, Accurate Docking and Scoring 1 Method and Assessment of Docking Accuracy, J Med Chem 47(7) 1739-1749... 

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