Three-dimensional molecular structure data

Figure 7.1 (a) The denatured conformation of the zinc metalloenzyme carbonic anhydrase and the ESI mass spectra obtained under acidic denaturing conditions, (b) The ESI mass spectra obtained under native-state conditions. The decon-voluted ESI mass spectra of carbonic anhydrase reveals the protein molecular weight. The three dimensional structure is protein Data Bank ID IBNl. 

Other recent advances that have impacted CADD include the growth in the quantity and quality of available molecular structure data. It has been estimated that three-dimensional (3D) data for more than a million small and large molecular models exist in machine-readable form at universities and companies around the world. Perhaps most important, a large body of experi-... 

The Notion of Three-Dimensional Molecular Structure Data... 

Inorganic Three-dimensional Structure Databases Molecular Docking and Structure-based Design Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Searching,... 

Several research groups have built models using theoretical desaiptors calculated only from the molecular structure. This approach has been proven to be particularly successful for the prediction of solubility without the need for descriptors of experimental data. Thus, it is also suitable for virtual data screening and library design. The descriptors include 2D (two-dimensional, or topological) descriptors, and 3D (three-dimensional, or geometric) descriptors, as well as electronic descriptors. 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

The ball and wire display is used for model building Although it is convenient for this purpose other model displays show three dimensional molecular structure more clearly and may be preferred The space filling display is unique m that it portrays a molecule as a set of atom centered spheres The individual sphere radii are taken from experi mental data and roughly correspond to the size of atomic electron clouds Thus the space filling display attempts to show how much space a molecule takes up... 

The demulsification data with four different demulsifiers for a crude oil-water system (Table I) support this conclusion. Structurally, the demulsifier PI and R0 are of moderate (MW 2,000-5,000) molecular weights, whereas PI and P2 are large (MW >50,000) three dimensional structures. 

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