Matt is a multiple protein structure alignment program. It uses local geometry to align segments of two sets of proteins, allowing limited bends in the backbones between the segments. If you use Matt, please cite: M. Menke, B. Berger, L. Cowen, "Matt: Local Flexibility Aids Protein Multiple Structure Alignment", PLOS Computational Biology, Vol. 4, No 1., 2008.

Matt is licensed under the GNU public license version 2.0. If you would like to license Matt in an enviroment where the GNU public license is unacceptable (such as inclusion in a non-GPL software package) comercial Matt licensing is available through the MIT and Tufts offices of Technology Transfer. Contact or for more information.

Matt is also mirrored at MIT:

This work was supported in part by National Science Foundation Information Technology Research for National Priorities grant (ASE+NHS)(dms)0428715.

New! Try out Matt on a new webserver designed by Anoop Kumar.

Matt Version 1.0:

The new version of Matt supports partial alignments when > 2 structures are input.

Source: tar, zip.

Windows OpenMP Binary (Needed VC 2005 SP1 runtime dlls)

Matt Version 0.97:

This is the version that produced the results in our paper

Source: tar, zip.

Windows OpenMP Binary

Readme (Also included in all archives)

Results on data sets used in the paper:

Homstrad results
Sabmark superfamily results

The Homstrad results include only the sets of structures used in the paper, so sets with only 2 structures as well as a few newer sets are not listed.

Currently Matt makes no effort to align residues not in the common core of all the aligned structures.

The Jmol/Rasmol scripts will highlight the core residues of each structure in a different color.

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