Alignment free methods

Finally, it is worth mentioning that alignment-free methods for evaluating molecular similarity have been tested [45]. Recently, the question about the necessary positive definite nature the MQSM matrices must possess has been put forward and a building up algorithm for a set of molecular structures has been described [53]. 

Although Fastcompare is an alignment-free method, the sequence randomization procedure previously described requires the application of global alignment. We have used ClustalW (14), available at http //www.ebi.ac.uk/clustalw/. ClustalW must be installed locally, before running the randomization scripts. 

As a final note, on several occasions, alignment-free methods have been used to quantify molecular similarity in the field of molecular quantum similarity, these methods have not yet fovmd extensive application. One method to obtain molecular quantum similarity measures without the need for molecular alignment was published by Boon et al. They use statistical techniques, more specifically, the autocorrelation function. This technique offers an interesting alternative method for similarity studies by removing completely the important obstacle of molecular alignment. 

The basic idea of alignment-free shape matching is that a set of rotation- and translation-free descriptors are calculated for con-formers under consideration, and then some similarity measure is devised to quantify the similarity between two molecular objects. Zauhar s shape signatures (45), Breneman s PEST and PESD methods (54-56), the USR (ultrafast shape recognition) method... 

Renner S, Fechner U, Schneider G. Alignment-free pharmacophore patterns - A correlation-vector approach. In Langer T, Floffmann RD, editors. Pharmacophores and Pharmacophore Searches Methods and Principles in Medicinal Chemistry). Weinheim Wiley-VCH 2006. p 49-80. 

A universal way of tackling the problem of molecular flexibility was suggested in paper [65] for kernel-based methods. It consists in averaging kernels over all conformations for each molecule. This approach is however computationally feasible only for veiy small number of conformations per molecule. Indeed, consideration of only 20 conformations for each molecule results in the necessity to consider 400 pairs of conformations in order to fill each cell in kernel matrix. In addition to huge computational burden, this approach does not solve the problem of ahgnment and therefore applicable only for alignment-free approaches. 

Preparation methods for PCNTs have been reviewed in the context of parameters which may lead to large-scale MWCNT synthesis free of by-products. It is noteworthy that the formation of aligned CNTs is currently an active area of research in conjunction with PCNT preparation. The use of SWCNTs and/or MWCNTs in electronic devices are being developed. As yet it has not proved possible to produce CNTs with diameters and helicities to order. The formation of SWCNTs by the PCNT process has not yet been reported and it is of interest to examine whether this process can be used to prepare them. 

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