Flexible Docking with Full Flexibility

Although the ensemble enriching multiple copy MD approach is currently too demanding in terms of computational resources to be applied to a large set of protein-protein complexes, it shows that simulations with fully flexible proteins can be useful computational aids when no a priori limitations on flexibility should be made. 

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Davis. l.W. and Baker, D. (2009) RosettaLigand docking with full ligand and receptor flexibility. Journal of Molecular Biology, 385, 381-392. 

Meiler J, Baker D (2006) ROSETTAEIGAND protein-small molecule docking with full side-chain flexibility. Proteins Str, Eunct, Bioinform 65(3) 538-548. doi 10.1002/prot.21086... 

Bcl-2 is one of the many factors that control apoptosis, and overexpression of Bcl-2 has been observed in many different cancers. A homology model of Bcl-2 was derived from the NMR 3D structure of the Bcl-XL complex with a Bak BH3 peptide. This model served to search the NCI 3D database of 206,876 organic compounds for potential Bcl-2 inhibitors, which bind to the Bak BH3 binding site of Bcl-2. Full conformational flexibility of the ligands was taken into account in the program DOCK. Thirty-five potential inhibitors were tested, and seven of them had IC50 values from 1.6 to W.OpM. One of... 

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