Structure template

B. Aligning the Target Sequence with the Template Structures... 

Although comparative modeling is the most accurate modeling approach, it is limited by its absolute need for a related template structure. For more than half of the proteins and two-thirds of domains, a suitable template structure cannot be detected or is not yet known [9,11]. In those cases where no useful template is available, the ab initio methods are the only alternative. These methods are currently limited to small proteins and at best result only in coarse models with an RMSD error for the atoms that is greater than 4 A. However, one of the most impressive recent improvements in the field of protein structure modeling has occurred in ab initio prediction [155-157]. 

Distortions or shifts of a region that is aligned correctly with the template structures. 

Parke-Davis targeted a template structure with no formal charge replacing the Glu-Glu dipeptide bridging pTyr with lie (pTyr+3), since the X-ray structure of SH2-peptide complexes suggested that the contribution of the two charged... 

A pharmacophore hypothesis can be derived from a series of known ligands and their common 3D-features. The pharmacophore is constructed by superimposing energetically favorable conformations of all ligands according to their consensus in structural features. The template structure for the superposition should fulfill two criteria ... 

The nanoreplication of functional nanostructures has also been achieved through other block copolymer-templated structures. De Boer et al. [35] applied honeycomb-structured films of rod-coil block copolymer as patterned templates to replicate hexagonally packed arrays of aluminum cups on the substrate surfaces (Fig. 10b). Nguyen et al. [237] embedded semiconducting polymers in the channels of oriented hexagonal nanoporous silica and used this nanoscale architecture to control the energy transfer for potential optoelectronic applications. 

Schenborn ET, Mierendorf RC. 1985. A novel transcription property of SP6 and T7 RNA polymerases Dependence on template structure. Nucl Acids Res 13 6223. 

The design of a functional protease mimic thus has to be considered to be too difficult a problem for the time being. In contrast, the successful design strategies to date are based on relatively simple concepts that do not require several residues to be in the correct conformations simultaneously and where the chemistries and template structures are compatible with the intended functions. 

Fig. 2.9 Template structures for the intermediate in catalytic asymmetric hydroboration with alkene, ligand, catechoborane and hydride coordinated, (a) R-BINAP and (b) R-QUINAP. E-propenylbenzene is illustrated to show the increased steric hindrance to the alkene in the BINAP case.

Sequence Identity (%) Among Isoenzymes Commonly Used as Template Structures for Homology Modeling and Major Human CYPs Calculated by Clustal W (43)... 

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