MM-align is an algorithm for structurally aligning a pair of multiple-chain protein complexes. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. An optimal alignment between two complexes, as well as the overall TM-score, will be reported.

News: MM-align was extended to US-align which enables monomeric and complex structural alignments between proteins, RNAs and DNAs.

Structure 1 in PDB or PDBx/mmCIF format.
Please copy and paste your structure file here. Example input

Or upload the structure file:
Structure 2 in PDB or PDBx/mmCIF format.
Please copy and paste your structure file here. Example input

Or upload the structure file:
Advanced options
• How many models to read from a multi-model structure file? [Help with asymetric unit and biological assembly]
  Only read the first model. Recommended for alignment of asymetric units. ("-ter 1" option of the MM-align++ program.)
  Read all models. Recommended for alignment of biological assemblies, i.e. biological units. ("-ter 0" option of the MM-align++ program)
  

• Click MMalign.cpp (2021/08/16 version) to download the latest source code of MM-align++ in C++. You can compile the program in your Linux computer by
  
  $ g++ -static -O3 -ffast-math -o MMalign MMalign.cpp
  or
  $ make
• Click MMalign.zip to download the Linux 64 bit executable of MMalign++. Nevertheless, you are 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).
• Click MMalign.f (2019/10/16 version) and MMalign.gz to download the old Fortran version of MM-align source code and Linux 64 bit executable compiled by g77, respectively. You can compile the program in your Linux computer by
  
  $ gfortran -static -O3 -ffast-math -lm -o MMalign MMalign.f (recommended)
  or
  $ g77 -static -O3 -lm -o MMalign MMalign.f
  Please note that the old Fortran version of MM-align will not be maintained in the future. You are encouraged to update to MM-align++ written in C++ (see above).

• Click benchmark.txt 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 align protein complexes using the "-ter 1" or "-ter 0" option of the C++ version of TM-align, which joins all chains, this will lead to suboptimal alignments with unphysical cross alignments. Therefore, the best result will be obtained if one uses TM-align and MM-align for monomer and multimer structures, respectively.
• The latest updates of the MM-align program:
  • 2021/08/16: MM-align has been updated to MM-align++, with major updates including
    • Alignment of hybrid complexes consisting of both protein and nucleic acids, such as ribosomes, is now supported.
    • A new assignment algorithm is implemented for fast chain-level correspondence search to improve the accuracy of large homo-oligomers alignment.
    • Support for the PDBx/mmCIF format is newly included in MM-align++, in addition to the legacy PDB format used in MM-align.
    • Fixed issue in the old MM-align program where alignments were not generated a pair of complex structures have divergent structures.
    • The new MM-align++ program includes five different chain-level initial alignment methods to ensure accurate initial alignment generation, in contrast to the old MM-align program that only implements one chain-level initial alignment (gapless threading).
  • 2019/10/16: Add a new option to read multi-model structure file.
  • 2019/10/13: Improves chain assignment for oligomer alignment by MM-align++.
  • 2019/10/07: MM-align++, i.e., C++ version of MM-align was officially released.
  • 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 alignment.

• 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] and [Supporting Materials]).