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Conformance Templates

Lists of conformational templates are assigned to all conformational units, which are taken from a library. [Pg.2981]

The most important requirement for CoMFA and CoMSlA studies is that the 3D structures to be analyzed are aligned according to a suitable conformational template, which is assumed to be a bioactive conformation. To make the 3D-QSAR predicting models more relevant to the real active site of the enzyme, a flexible molecular docking approach was carried out. The docking conformations were assumed to be the actual bioactive binding conformations. [Pg.324]

As a template for an intermediate conformation of protein kinase, the crystal structure of the binary complex of cAPK with adenosine (Ibkx.pdb in the Protein Data Bank) was used. As templates for open conformations... [Pg.68]

In the next step, the third conformation is determined by searching for the geome-t y furthest from the first two conformations. This procedure is repeated unless a user-defined number of structures has been generated or no 3D templates arc left to combine. [Pg.109]

Backbone generation is the first step in building a three-dimensional model of the protein. First, it is necessary to find structurally conserved regions (SCR) in the backbone. Next, place them in space with an orientation and conformation best matching those of the template. Single amino acid exchanges are assumed not to affect the tertiary structure. This often results in having sections of the model compound that are unconnected. [Pg.188]

Fig. 8. Rephcation. The amino adenosine X and the pentafluorophenyl ester Y form a hydrogen-bonded dimer XY, prior to reaction between the amine and the activated ester groups (shown in the circle). The reaction product is a <7 -amide conformer cis-Z that isomeri2es to the more stable trans- acnide Z. The rephcative process is cataly2ed by the reaction product Z (also referred to as the template). First, a termolecular complex XYZ is formed from X, Y, and Z. Fig. 8. Rephcation. The amino adenosine X and the pentafluorophenyl ester Y form a hydrogen-bonded dimer XY, prior to reaction between the amine and the activated ester groups (shown in the circle). The reaction product is a <7 -amide conformer cis-Z that isomeri2es to the more stable trans- acnide Z. The rephcative process is cataly2ed by the reaction product Z (also referred to as the template). First, a termolecular complex XYZ is formed from X, Y, and Z.

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Template-assembled synthetic protein conformation

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