D Structure Generation

Table 3 3-D Structure Generation Comparison of CONCORD and CORINA Using...

Bultinck P, Augustynen S, Hilbers HW, Moret EE, Tollenaere JP. Generate a program for 3-D structure generation and conformational analysis of peptides and peptidomi-metics. J Comput Chem 2002 23 746-754. 

D structures generated from 2-D structures crystal structures (Cambridge and internal) structures generated from molecular modeling... 

Metzler W J, Hare D R and Pardi A 1989 Limited sampling of conformational space by the distance geometry algorithm implications for structures generated from NMR data Bioohemistry 2S 7045-52... 

A R, D P Dolata and K Prout 1990. Automated Conformational Analysis and Structure Generation Algorithms for Molecular Perception. Journal of Chemical Information and Computer Science 30 316-324. 

As it was mentioned in Section 9.4.1, 3D structures generated by DG have to be optimized. For this purpose, MD is a well-suited tool. In addition, MD structure calculations can also be performed if no coarse structural model exists. In both cases, pairwise atom distances obtained from NMR measurements are directly used in the MD computations in order to restrain the degrees of motional freedom of defined atoms (rMD Section 9.4.2.4). To make sure that a calculated molecular conformation is rehable, the time-averaged 3D structure must be stable in a free MD run (fMD Sechon 9.4.2.5J where the distance restraints are removed and the molecule is surrounded by expMcit solvent which was also used in the NMR measurement Before both procedures are described in detail the general preparation of an MD run (Section 9.4.2.1), simulations in vacuo (Section 9.4.2.2) and the handling of distance restraints in a MD calculation (Section 9.4.2.3) are treated. Finally, a short overview of the SA technique as a special M D method is given in Sechon 9.4.2.6. 

Leatherface is a 2-D molecular editor that modifies properties of atoms and bonds in molecular connection tables according to rules specified by the user. Unlike Permute, Leatherface encodes no chemical knowledge and neither processes nor generates 3-D structures. Its real strength is that it allows the user to impose a very detailed and precisely specified chemical view on large numbers of connection tables. 

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