[gmx-users] Structural alignment of different proteins

[Ran Friedman]

Dear GMX users,

I uploaded a wrapper to run the Multiprot program using output from
Gromacs to the user contributions in the GMX site. Multiprot,
http://bioinfo3d.cs.tau.ac.il/MultiProt/ , performs structural alignment
based on geometry, not sequence, and thus it allows the alignment of two
proteins that differ in sequence. The alignment is performed over a
subset of the atoms which geometrically match.

The wrapper program, do_multipriot, uses multiprot to calculate the rms
between the trajectory and a reference protein and gives the number of
aligned residues as well. It's also possible to extract the aligned
trajectory. As in the case of do_dssp, multiprot is not distributed in
the contribution since it's not gpl. However, it is free for academic
users and can be downloaded from the multiprot site.

Hope other users will find this useful.

Ran.

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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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