Molecular replacement protocols

The computational requirements of these calculations are relatively modest on modern computers. However, some groups have exploited computer power to design ambitious molecular replacement protocols in which many models are assessed in parallel (see Section 12.6). 

Out of the work with HT-XPIPE it became clear to the consortium that there was a need to expand the automated molecular replacement protocol embodied in HT-XPIPE to handle scenarios in which either the target was a new project or ligand-binding caused a packing change in the protein that... 

Protocol 7.3 A typical molecular replacement session using AMoRe (Navaza, 2001) ... 

The integrated molecular replacement method comparison of automatic protocols... 

Figure 7.3 General flow chart for an Integrated molecular replacement structure solution protocol.

Recent achievements in molecular biology have created multiple methods that can be utilized to construct mutants by allelic replacements in different bacteria. A variety of temperature-sensitive plasmids, antibiotics resistance markers, and transformation protocols are now available. 

Traditional methods to generate peptide maps involve fractionation of complex mixtures of peptides in a protein digest either with one-dimensional SDS-PAGE or RP-HPLC [28,29]. The mass spectrometry peptide-mapping protocol, in principle, is similar to these techniques, but it provides an added dimension of structure-specific data (i.e., the molecular mass). MALDI-MS [30,31], ESl-MS [32], LC/ESI-MS [33], and CE/ESI-MS [34] have currently replaced the traditional biochemical approaches. MALDI allows the direct analysis of unfractionated protein digests. The commonly used matrices are sinapinic acid, a-cyano-4-hydroxy cinnamic acid (a-CHCA), and 2,5-dihydroxybenzoic acid (DHB). 

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