Three-dimensional structure generation

Green DVS. Automated three-dimensional structure generation. In Martin YC and Willett P, editors, Designing bioactive molecules. Three-dimensional techniques and applications. Washington DC, American Chemical Society, 1998 47-71. 

Three-dimensional structures generated from the Chemical Abstracts registry file by CONCORD. 

Self-assembled molecular capsules are three-dimensional structures generated through reversible, noncovalent interactions such as hydrogen bonding between complementary subunits. They circumvent many problems of covalent capsules, such as multistep and complicated synthetic methods and lack of versatility. Therefore, recent researches are focused on self-assembled systans [2], Micelles, emulsions, vesicles, and noncovalent molecular capsules are examples of self-assembled NRs [2],... 

Jia, B., Buso, D., van Embden, J., Li, J and Gu, M. (2010) Highly non-linear quantum dot doped nanocomposites for functional three-dimensional structures generated by two-photon polymerization. Adv. Mater., 22, 2463-2467. 

The type of features that are typically used in our size and shape searching are generic 3D triangle and 3D tetrangle features which are derived from 3D structures generated by the CONCORD program (see Three-dimensional Structure Generation Automation). 

Stereochemistry Representation and Manipulation Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Generation Automation Three-dimensional Structure Searching Topological Indices Topological Methods in Chemical Structure and Bonding. 

Cambridge Structural Database De Novo Ligand Design Pharmacophore and Drug Discovery Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structure Databases Three-dimensional Structure Generation Automation Three-dimensional Structure Searching. 

Gasteiger and co-authors recently suggested a new approach. They developed a molecular transform, derived from an equation used in electron diffraction studies, that allows the presentation of the 3D structure of a molecule by a fixed (constant) number of variables. On the other hand, a generator of 3D structures of organic compounds was created (see Three-dimensional Structure Generation Automation). This made it possible to study the correlations between 3D structures and infrared spectra using ANN. 

Table 4 The 45 Combinations of Base Pairing Patterns Found in the Set of Loop 785-797 Three-dimensional Structures Generated by the MC-SYM Program...

Generate a three-dimensional molecular model (see Three-dimensional Structure Generation Automation) for each compound ... 

The structure of each compound is stored as a connection table. A molecular models is generated for each stored structure using molecular mechanics model building such as MM2, the semiempirical method MOPAC 6.0, or specialized methods such as a recently developed extended Hiickel method. Three-dimensional structures can also be generated directly from their connection tables by structure generators (see Three-dimensional Structure Generation Automation) such as concord or CORINA. Some approaches to QSPR use only descriptors derived from the topological representation of the molecular structures, and in this case the development of three-dimensional molecular models is not necessary. 

These 3D models describe a fixed conformation. The only permissible motions of this model are 3D translations and rotations of the molecule as a whole. The relative mobility of parts of an individual molecule can also be described on the basis of its 3D coordinates (see Three-dimensional Structure Generation Automation). It requires the specification of so-called rotatable bonds to record permissible or feasible changes of the conformation. Conformational analysis programs use such a model as their internal problem representation. Partially flexible ring systems require additional sophistication to be modeled adequately using this approach. 

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