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TM-align unified package download

This package unifies protein structure alignment and RNA structure alignment into the standard TM-align program for single chain structure alignment, MM-align program for multi-chain structure alignment, and TM-score program for sequence dependent structure superposition.

Download

• Download C++ source code of TM-align unified package. You need g++ to compile:
  $ g++ -O3 -ffast-math -o TMalign TMalign.cpp -static
  $ g++ -O3 -ffast-math -o MMalign MMalign.cpp -static
  $ g++ -O3 -ffast-math -o TMscore TMscore.cpp -static
  
  or
  
  $ make TMalign MMalign TMscore
  
  The "-static" flag should be deleted on Mac, which does not support static build.
  
• Download pre-compiled executable for 64bit Linux. Nevetheless, it is recommended that you download the source code and compile it on your machine, which gives higher speed to run the program.

New features

All new features can be explored by running the programs with "-h" argument.

• Automatic detection and alignment of protein, RNA, and DNA
• Native support for both PDB and PDBx/mmCIF format.
• In addition to reading uncompressed files, this package can also read ".gz" and/or ".bz2" compressed files, if your system supports "zcat" and/or "bzcat" commands, respectively.
• Optionally runs fTM-align algorithm for fast but slightly inaccurate alignment via the "-fast" flag.
• Optional alignment of multiple chains in one file (via the "-split" and "-ter" flags) or multiple files in one folder (via the "-dir", "-dir1", "-dir2" and "-suffix" flags).
• Optionally performs alignment by circular permutation, via the "-cp" flag.
• Optionally performs alignment of mirror structure, via the "-mirror" and "-het" flags.

References

If you find this package useful, please cite at least one of the following papers. Sha et al (2019) is the primary citation for RNA/DNA structure alignment, while Zhang and Skolnick (2005) is the primary citation for protein structure alignment.

• Sha Gong, Chengxin Zhang, Yang Zhang. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-score_RNA. Bioinformatics, btz282 (2019).
• Yang Zhang, Jeffrey Skolnick. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research, 33: 2302 (2005).
• Yang Zhang, Jeffrey Skolnick. Scoring Function for Automated Assessment of Protein Structure Template Quality. Proteins: Structure, Function, and Bioinformatics, 57: 702 (2004).
• Srayanta Mukherjee, Yang Zhang. MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Research, 37: e83 (2009).

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