Protein-ligand complexes, molecular

Lugovskoy AA, et al. A novel approach for characterizing protein ligand complexes molecular basis for specificity of small-molecule Bcl-2 inhibitors. J. Am. Chem. Soc. 2002 124 1234-1240. 

Molecular dynamics simulation methods are currently the most popular approaches. This method is for the analysis of protein flexibility and dynamic properties of molecular systems. With respect to docking, these simulations could provide a realistic view of the docking process, however, these calculations are still out of reach. Therefore, dynamical simulations during the docking process are limited to the protein-ligand complexes. Molecular dynamical simulations are often... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Bonaccorsi ct al. [204 defined for the first time the molecular electrostatic potential (MEP), wdicli is dearly tfie most important and most used property (Figure 2-125c. The clcctro.static potential helps to identify molecular regions that arc significant for the reactivity of compounds. Furthermore, the MEP is decisive for the formation of protein-ligand complexes. Detailed information is given in Ref [205]. 

I-J 1994. The Development of a Simple Empirical Scoring Fimction to Estimate the Binding istant for a Protein-ligand Complex of Known Three-Dimensional Structure. Journal of nputer-Aided Molecular Design 8 243-256. 

Molecular recognition of protein-ligand complexes and drug design 97CRV1369. 

Bohm HI, Klebe G. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs Angew Chem Int Ed Engl 1996 35 2589-614. 

Babine RE, Bender SL. Molecular recognition of protein-ligand complexes applications to drug design. Chem Rev 1997 97 1359-472. 

ALIS measures the MS response of the ligand following its dissociation from the protein-ligand complex. Therefore, the magnitude of the MS response corresponds to the equilibrium concentration of the receptor-ligand complex concentration [ S] times the compound s MS calibration factor Cms, which depends on the ionization efficiency and other molecular properties of the ligand ... 

---