Methods for protein-ligand docking

Hoffmann D, Kramer B, Washio T et al (1999) Two-stage method for protein-ligand docking. J Med Chem 42(21) 4422-4433... 

Huang SY, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein-ligand docking recent advances and future directions. Phys Chem Chem Phys 12(40) 12899-12908... 

Chem., 42, 4422 (1999). Two-Stage Method for Protein—Ligand Docking. 

Fukunishi, H., Teramoto, R., Takada, T, and Shimada, J. (2008) Bootstrap-based consensus scoring method for protein-ligand docking. Journal of Chemical Information and Modeling, 48, 988-996. 

In CASP II (Critical Assessment of Methods of Protein Structure Prediction Round II), a new prediction section on protein-ligand docking was introduced [154]. Several groups participated and submitted up to three models for some of the seven protein-ligand complexes (see [155-158] for reports). For each target, the 3D structure of the protein and the 2D structure of the ligand was given to the participants. All complexes were unpublished before the submission deadline. 

Molecular dynamics methods are primarily used for the refinement of structural models (Li et al., 1997) or the analysis of molecular interactions (Cappelli et al., 1996 Kothekar et al., 1998). In both cases the time scales to be simulated are within range of current computing technology. Another application area is the study of allosteric movements of proteins (Tanner et al., 1993). Molecular Dynamics approaches to protein-ligand docking are described in Chapter 7 of Volume I. 

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