Docking methods protein flexibility

Rarey, M., Kramer, B., Lengauer, T., Klebe, G. A fast flexible docking method using an incremental construction algorithm. /. Mol. Biol. 1996, 263, 470-489. Joseph-McCarthy, D., Alvarez, J.C. Automated generation of MCSS-derived phar-macophoric DOCK site points for searching multiconformation databases. Proteins 2003, 53, 189-202. 

Sampling of the biomolecular conformations is usually performed using MD simulations or Monte Carlo methods (61, 62). The protonation state of titrateable amino acids can be treated with constant pH dynamics, QM/MM calculations, or continuum electrostatics methods (61, 62). Formation of a protein-protein encounter complex is often studied using Brownian dynamics (63). Studies of protein-protein docking involve electrostatic potential analysis and, more recently, protein flexibility models, for example normal mode analysis (64). 

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