LSim superposes macromolecular electron densities and computes a structural similarity score. Its computations scale linearly with the size of the molecules being compared.
The LSim alignments are conceptually unrelated to biochemical structural elements and, therefore, are unbiased and appropriate for structure-only protein similarity studies.
Installation:
Unpack the distribution file:
tar -xzvf lsim-linux.tar.gz
Move to file directory:
cd lsim.1.0.0
Copy, move or link the executable file lsim to an appropriate location -and make sure lsim is accessible through the PATH environment variable-, e.g.:
cp lsim /usr/local/bin
Set variable LSIMDIR to point to the chosen LSim directory, e.g.:
setenv LSIMDIR /home/olaguer/progs/lsim.1.0.0
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