Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein...Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein-protein interactions occur on comparatively fiat regions whereas protein-ligand bindings involve crevices. In the search for such sites various approaches have been designed and developed each of which is algorithmically unique. The use of grid units or voxels has been demonstrated in early studies with relatively good results obtained. We present here an approximated approach comprising of the use of voxels and computer vision methods in the search for ligand-binding areas. Each test protein is modelled and analysed in 2D with all corresponding residues graphically presented for successfully identified sites. The study was carried out on 2 sets of proteins： FK506-bound proteins and heme-bound proteins with promising results obtained for all test cases.展开更多
Hydrophobic fluorescence:Tan and his colleagues recently introduced a brand new chemotype of environment-sensitive fluorescent turn-on probes to detect the hydrophobic ligand-binding domain by using SBD fluorophore.Th...Hydrophobic fluorescence:Tan and his colleagues recently introduced a brand new chemotype of environment-sensitive fluorescent turn-on probes to detect the hydrophobic ligand-binding domain by using SBD fluorophore.The design strategy described in this report generalized the environment sensitivity turn-on mechanism to recognize a specific protein,which provides a robust breakthrough for interchanging fluorescence in conventional small-molecule fluorescent imaging.展开更多
文摘Most protein-ligand interactions take place on surfaces and include but not limited to factors such as chemical composition, hydrophobicity, electronegavitiy and shape complementarity. Past studies showed that protein-protein interactions occur on comparatively fiat regions whereas protein-ligand bindings involve crevices. In the search for such sites various approaches have been designed and developed each of which is algorithmically unique. The use of grid units or voxels has been demonstrated in early studies with relatively good results obtained. We present here an approximated approach comprising of the use of voxels and computer vision methods in the search for ligand-binding areas. Each test protein is modelled and analysed in 2D with all corresponding residues graphically presented for successfully identified sites. The study was carried out on 2 sets of proteins： FK506-bound proteins and heme-bound proteins with promising results obtained for all test cases.
基金supported by the National Natural Science Foundation of China (81370085)the Program of New Century Excellent Talents in University (NCET-11-0306)+2 种基金the Fok Ying Tong Education Foundation (122036)the Shandong Natural Science Foundation (JQ201019)the Independent Innovation Foundation of Shandong University (2010JQ005 and 2012JC002).
文摘Hydrophobic fluorescence:Tan and his colleagues recently introduced a brand new chemotype of environment-sensitive fluorescent turn-on probes to detect the hydrophobic ligand-binding domain by using SBD fluorophore.The design strategy described in this report generalized the environment sensitivity turn-on mechanism to recognize a specific protein,which provides a robust breakthrough for interchanging fluorescence in conventional small-molecule fluorescent imaging.
