Protein docking packages

Table 16.4 Some protein docking packages and online flexibility investigation.

Given the multitude of approaches now used to dock small molecules and peptides to proteins, why should the protein-protein docking problem require its own approaches Could one make do with the software packages developed for these related problems Unfortunately, the answer is usually no. 

Trosset J-Y, Scheraga HA (1999) Prodock software package for protein modeling and docking. J Comp Chem 20 412-427... 

Download the AutoDock 4.2 package from http //www.aut-odock.scripps.edu/ to dock the modeling protein structure and small molecules for virtual screening for potential antibiotics binding the active site. The structure of one such potential antibiotic (enoxacin) is shown in Fig. 4. If we assume that a given pocket is important for the function of the protein, we screen for small molecules that can dock to that site. 

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