Ligand binding modes

The practical utility of the target-structure-based approach in the design of chemical libraries is still limited because of the requirement of quality crystallographic data, detailed knowledge of the ligand binding mode, and... 

According to the peculiarities of the ligand binding mode and the specificity profiles described in Sects. 2.4 and 2.5, respectively, the lead design problem can be separated into individual subtopics as shown in Fig. 9. 

Ishiguro, M. (2004) Ligand-binding modes in cationic biogenic amine receptors. Chembiochem A European Journal of Chemical Biology, 5, 1210. 

Figure 16 Comparison of exogenous ligand binding modes In l/2-met hemocyanln (left) and 1/2-met laccase (right).

The remainder of this chapter will focus on some of the applications of structural informatics and the TIP database. We will use the Key Applications column in Fig. 2 as an outline, describing the applications enabled by understanding 1) protein structural relationships 2) binding site relationships and 3) ligand binding mode relationships. 

Kelly, M.D., Mancera R.L., Expanded interaction fingerprint method for anlays-ing ligand binding modes in docking and structure-based dmg design. J. 

Root mean square) deviation from a reference structure (what is the ligand binding mode compared with other [homologous] ligands ) ... 

Figure 2 Metal-ligand binding modes found in cyanide complexes...

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