is an algorithm for structurally aligning multiple-chain
The algorithm is built on a heuristic iteration of a modified
Needleman-Wunsch dynamic programming (DP) algorithm,
with the alignment score specified by the inter-complex residue distances.
The multiple chains in each complex are first joined,
in every possible order, and then simultaneously aligned with cross-chain
The alignments of interface residues are enhanced by an interface-specific
An optimal alignment between two complexes, as well as the overall
will be reported for each comparison.
- Format of input files:
Each complex should be in the standard
with the two chains seperated by a "TER" (Click here for an example of the format).
Structure 1 in
PDB format (mandatory):
Please copy and paste your structure file here. Sample input
- Click MMalign.f to download the newest version of
the source code of MM-align
coded in Fortran77. You can compile the program in your Linux computer by
>gfortran -static -O3 -ffast-math -lm -o MMalign MMalign.f (recommended)
>g77 -static -O3 -lm -o MMalign MMalign.f
- Click MMalign to download the F77 executable program
for Linux system. Nevetheless, it is strongly recommended to download the
MM-align source code and compile it on your machine, which gives you higher
speed to run the program (See above step).
MM-align other information
- Click MM-align Help
to view a brief instruction on how to run MM-align program.
- Click benchmark to download a list of 205 non-homologous proteins
taken from PDB (sequence identity<30%) and a larger dimer dataset;
these two sets of proteins was used as a benchmark test of MM-align method.
- What is the difference between MM-score and MM-align?
TM-align is for
aligning monomer protein structures while MM-align is designed for
aligning multiple-chain protein complex structures.
Although one can still use TM-align to align protein complexes after
manually joining the chains, this will lead to suboptimal alignments with
unphysical cross alignments.
Therefore, the best result will be obtained if one uses TM-align
to monomer structures and MM-align for multimer structures.
- The newest updates of MM-align program:
- 2013/08/15: Fixed a number of compiler bugs
- 2009/09/30: A bug in the output display was fixed
- 2009/01/27: Extension from dimer to multimer align
- S. Mukherjee, Y. Zhang,
MM-align: a quick algorithm for aligning multiple-chain protein complex
structures using iterative dynamic programming.
Nucleic Acids Research 2009; 37: e83
PDF file and supporting materials).