Molecular structure biological data integration

PubChem archives the molecular structure and bioassay data from the MLSCN and other contributors. PubChem provides search, retrieval, and data analysis tools to optimize the utility of these results. PubChem further enhances the research utility of the MLSCN output by including other public sources of chemical structure and bioactivity information and by integration of this data with other NIH biomedical knowledgebases. The primary aim of PubChem is to provide a public on-line resource of comprehensive information on the biological activities of small molecules accessible to molecular biologists as well as computational and medicinal chemists. 

The next step up in integration places as much information as possible in the chemical structure or reaction DBMS. For example, Molecular Design Limited s MACCS system has been used to store structures, reactions, biology, spectra, inventory, and document index information. This approach provides a good degree of data integration but suffers from poor performance for large databases. Additionally, the retrieval capabilities of the structure DBMS are inadequate for certain types of information. 

Three-dimensional database searching is a powerful new tool for developing novel synthetic targets. This technique can be used in cases where an enzyme/receptor 3-D structure is known, or alternatively in the case where the enzyme/receptor structure is unknown. In the latter case an active compound or series of compounds can be used to develop a pharmacophore model. Because 3-D database searching requires biological data stored in 2-D databases and molecular modelling techniques, we expect to see increased integration of 2-D and 3-D database/ information systems. 

Myelin in situ has a water content of about 40%. The dry mass of both CNS and PNS myelin is characterized by a high proportion of lipid (70-85%) and, consequently, a low proportion of protein (15-30%). By comparison, most biological membranes have a higher ratio of proteins to lipids. The currently accepted view of membrane structure is that of a lipid bilayer with integral membrane proteins embedded in the bilayer and other extrinsic proteins attached to one surface or the other by weaker linkages. Proteins and lipids are asymmetrically distributed in this bilayer, with only partial asymmetry of the lipids. The proposed molecular architecture of the layered membranes of compact myelin fits such a concept (Fig. 4-11). Models of compact myelin are based on data from electron microscopy, immunostaining, X-ray diffraction, surface probes studies, structural abnormalities in mutant mice, correlations between structure and composition in various species, and predictions of protein structure from sequencing information [4]. 

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