Automated alignment methods

At the beginning of this chapter we will look into the different automated alignment methods as correct alignment is the first and most important prerequisite for a successful pharmacophore identification process. Further, we will elaborate how essential issues of pharmacophore modeling such as conformational search, pharmacophore feature definitions, compounds structure storage and screening are handled by various available software packages. 

The goal of automated alignment methods is to align multiple protein sequences correctly with minimal user input. Although the alignment parameters are selected by the user, they are typically the well-established similar-... 

Miigge, I., Podlogary, B.L. 3D Quantitative Structure-Activity Relationships of Biphenyl Carboxylic Acid MMP-3 Inhibitors Exploring Automated Docking as Alignment Method. Quant. Struct.-Act. Relat. 2001, 20, 215-223. 

Some of the typical applications were already mentioned in the second section when the alignment methods were discussed. The practical example presented in the sequel illustrates some of the advantages of the newly emerging alignment technology it is a non-contact, hot alignment, semi-automatic (with full automation possibility) and dynamic. 

Most sequence alignment methods are automated, but some are performed manually. Both the automated and the manual alignment of multiple chains is a challenging problem because of the myriad of alignment possibilities. The number of combinations for alignment is determined by raising the number of sequences by the number of amino acid residues of the longest sequence (Equation [1]). 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

An alternative method which can also be automated by the use of the Titertek supernatant harvester (see Appendix 3) involves the measurement of radioactive chromium released into the culture medium from killed cells. The harvester consists of a set of absorbent cylinders aligned so that they may be inserted into the wells of a microtitration plate (Appendix 3). Once the supernatant in the wells has been absorbed the cylinders are transferred to counting vials and the amount of radioactive chromium released from the cell monolayer is estimated. Cells take up 51 Cr sodium chromate rapidly and the excess is readily washed away by rinsing in culture medium. 

Automating a conventional tool may not be possible, may be cost prohibited, and may not significantly accelerate the experiment. The alternative is to develop a new tool/s with the time-saving capabilities discussed earlier i.e., reduced sample size and testing time. This route will eventually result in significant methods development to establish a correlation between the conventional test and the HT approach. Often the correlation is not one-to-one with the absolute value from the conventional tools, but the trends are normally aligned. The reality of HT is there is a hand full of HT tools available for evaluating the common properties of common polymers in common applications, and the tool owners will need to establish a correlation between one of these HT tool responses and the desired end-product performance characteristic they want to measure. 

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