Multiple receptor conformation

Totrov M, Abagyan R (2008) Flexible ligand docking to multiple receptor conformations a practical alternative. Curr Opin Struct Biol 18(2) 178-184... 

Fleksy [102] is a docking protocol that incorporates the FlexE docking [53] engine already described in Section 8.2.1.2. Given an experimental input structure, the protocol generates multiple receptor conformations to introduce receptor flexibility. For rule-based identified or alternatively user-defined residues, it extracts some most... 

Ferrari, A.M., Wei, B.Q., Costantino, L., and Shoichet, B.K. (2004) Softdockingand multiple receptor conformations in virtual screening. Journal of Medicinal Chemistry, 47, 5076-5084. 

Multiple receptor conformations http //abagyan.ucsd.edu/MRC/ Generate normal mode-guided multiple receptor conformations... 

M. Totrov and R. Abagyan, Flexible Ligand Docking to Multiple Receptor Conformations A Practical Alternative , Curr. Opin. Struct. Biol., 2008, 18, 178. 

Docking to multiple receptor conformations (sometimes abbreviated MRC [8]) can be applied on a set of conformations from any source. Experimentally different X-ray conformations or NMR solution stmctures can represent the same biomolecular system. NMR solution stmctures and conformations sampled during an MD simulation represent a valid thermodynamic ensemble, e.g., a canonical ensemble, for simulations with constant number of particles, volume, and temperature. Although, a collection of X-ray stmctures is not a valid thermodynamic ensemble, docking to multiple X-ray stmctures is sometimes also termed ensemble docking. 

Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A (2011) Systematic exploitation of multiple receptor conformations for virtual ligand screening. PloS One 6(5) el8845. 

The flexible docking protocol described in this work is a simple way to generate multiple receptor conformations that can be used to easily dock a large number of compounds. 

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