Applications Small Molecule-Protein Interaction

Finally, we have recently successfully applied MASPIT to the screening of cDNA libraries and to the identification of novel small molecule-protein interactions [64], These studies mark the beginning of the development of a broadly applicable M3H system that holds promise for future use in target identification and drug discovery. 

The calculation of binding free energies is arguably the most common application of PB methods. As described earlier, PB methods provide the electrostatic energies and are often supplemented with additional terms representing apolar and other interactions. These calculations are performed on a wide variety of complexes ranging from small molecule-protein interactions to protein-membrane interactions and the energy of supramolecular assembly. ... 

Hu L, Xu S, Pan C, Zou H, Jiang G (2007) Preparation of a biochip on porous silicon and application for label-free detection of small molecule-protein interactions. Rapid Commun Mass Spectrom RCM 21 1277-1281... 

Haapala M, Pol J, Saarela V, Arvola V, Kotiaho T, Ketola RA, Franssila S, Kauppila TJ, Kostiainen R (2007) Desorption atmospheric pressure photoionization. Anal Chem 79 7867-7872 Hsieh Y, Li F-B, Korfmacher WA (2010) Mapping pharmaceuticals in rat brain sections using MALDI imaging mass spectrometry. Methods Mol Biol 656 147-158 Hu LG, Xu SY, Pan CS, Zou HF, Jiang GB (2007) Preparation of a biochip on porous sihcon and application for label-free detection of small molecule-protein interactions. Rapid Commun Mass Spectrom 21 1277-1281... 

Application of H/D Exchange to Protein-Small Molecule Ligand Interactions... 

GAs or other methods from evolutionary computation are applied in various fields of chemistry Its tasks include the geometry optimization of conformations of small molecules, the elaboration of models for the prediction of properties or biological activities, the design of molecules de novo, the analysis of the interaction of proteins and their ligands, or the selection of descriptors [18]. The last application is explained briefly in Section 9.7.6. 

Although protein behavior in SDS-containing buffers is qualitatively different from small molecules, applications of MEKC-type conditions have been applied to many protein separations. In applications using uncoated capillaries, protein-wall interactions are eliminated because of the anionic character of SDS-protein complexes. In applications using coated capillaries with no EOF, the high electrophoretic mobility of SDS-protein complexes can decrease analysis time. 

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