Computational solvent mapping of protein

Landon, M.R., Lancia Jr., D.R., Yu, J., Thiel, S.C., Vajda, S. Identification of hot spots within drug-gable binding regions by computational solvent mapping of proteins. J. Med. Chem. 2007, 50, 1231 0. 

Kortvelyesi, T, Dennis. S.. Silberstein, M-, Brown, L., and Vajda. S. (2003) Algoritiims for computational solvent mapping of proteins. Proteins Structure, Function, and Genetics, 51, 340-351. 

HA. (2008) Automated clustering of probe molecules from solvent mapping of protein surfitces new algorithms applied to hot spot mapping and structure-based design. Journal of Computer-Aided Molecular Design, 22,727-736. 

Once an electron density map has become available, atoms may be fitted into the map by means of computer graphics to give an initial structural model of the protein. The quality of the electron density map and structural model may be improved through iterative structural refinement but will ultimately be limited by the resolution of the diffraction data. At low resolution, electron density maps have very few detailed features (Fig. 6), and tracing the protein chain can be rather difficult without some knowledge of the protein structure. At better than 3.0 A resolution, amino acid side chains can be recognized with the help of protein sequence information, while at better than 2.5 A resolution solvent molecules can be observed and added to the structural model with some confidence. As the resolution improves to better than 2.0 A resolution, fitting of individual atoms may be possible, and most of the... 

Dennis S, Kortvelyesi T, Vajda S (2002) Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci USA 99 4290-4295... 

---