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LovoAlign is a new protein structural alignment package. The methods used for structural alignment are based on Low Order Value Optimization (LOVO) theory. The use of LOVO theory led to the development of fast convergent algorithms that provide very robust optimization of scoring functions.

The structural alignment is highly customizable. Particular chains of each protein may be selected or, alternativelly, any atom selection (of main chain atoms or not) from each structure can be used. Therefore, the package can be used for general structural alignments of any kind.

Numerical experiments show that the LOVO algorithms implemented here provide the most reliable optimization of the STRUCTAL alignment while being very fast.

Simple input parameters can be used to align two structures, a single structure to a whole database, or to perform an all-on-all database structural alignment.

The current version of the LovoAlign software can be downloaded, with source codes, at no cost.