TM-align Update history

  • 2016/05/21: fixed a bug on conformation output (TMtools20160521.tar.gz).
  • 2015/09/14: optimize I/O and increased speed by ~100% (TMtools20150914.tar.gz).
  • 2014/06/01: Added 'TM.sup_all_atm_lig' to display ligand structures (TMtools20140601.tar.gz).
  • 2013/05/11: Fix a bug in array overflow (TMtools20130511.tar.gz).
  • 2013/05/08: Update TM-align so that it can read all alternate location indicators and residue insertions (TMtools20130508.tar.gz).
  • 2012/07/07: Add an option '-I align.txt' to allow user to STICK TO the inital alignment. This is different from '-i align.txt' where initial alignment can be optimized. (TMtools20120707.tar.gz).
  • 2012/05/07: Improved RMSD calculation subroutine which speeds up TM-algin program by 10%. (TMtools20120507.tar.gz).
  • 2012/04/19: Add additional output file 'TM.sup_atm' for showing all-atom superposition while 'TM.sup' and 'TM.sup_all' are only for C-alpha traces (TMtools20120419.tar.gz).
  • 2012/04/17: Add an option '-m matrix.txt' to output the rotation matrix in separate file, drop-off secondary-structure smooth procedure, and add one iteration in initial5. This change increases the alignment accuracy (TM-score) by 2%. (TMtools20120417.tar.gz).
  • 2012/04/16: Add an option to allow user to specify seed alignments, e.g. '-i align.txt'. This is used together with other inherent TM-align seeds. An example of the fasta file can be seen at http://zhanglab.ccmb.med.umich.edu/TM-align/align.txt. (TMtools20120416.tar.gz).
  • 2012/01/24: Fix a bug for secondary structure definition (TMtools20120124.tar.gz).
  • 2011/10/11: Distance cutoff for gap is increased from 3.85A to 4.25A. Added 'TMalign -v' to allow user to check version number. (TMtools20111012.tar.gz).
  • 2011/10/11: A new scale (d0) was introduced for alignment search. This is to mainly improve alignment selection for small proteins (e.g. L<50 residues) but also increase alignment coverage of larger proteins. Second, TM-align output format is changed and two TM-scores normalized by both chains are reported. (TMtools20111011.tar.gz).
  • 2011/09/03: A new option "-d" is added to allow users to change TM-score normalization scale. A version number is attached to the program from now on (TMtools20110903.tar.gz).
  • 2011/01/30: An open source license is attached to the program (TMtools20110130.tar.gz).
  • 2011/01/24: Fixed a bug on output file name created on 2011/01/03.
  • 2011/01/03: The length of pdb file names were extended to 500.
  • 2010/08/02: A new RMSD matrix was used to remove obsolete statements. Staled subroutines were deleted.
  • 2009/08/20: A bug for asymmetry alignment result was fixed.
  • 2009/03/14: A new initial alignment was added and previous initial alignments are further enhanced. This change increased accuracy by 4% but increases CPU cost by 40%.
  • 2007/10/16: A bug for irregular bond-length models was fixed.
  • 2007/09/19: added a new feature alignment to deal with the problem of aligning fractional structures (e.g. protein interfaces).
  • 2007/05/23: added additional output file 'TM.sup_all' for showing all atoms while 'TM.sup' is only for aligned atoms
  • 2007/04/18: added options with TM-score normalized by average length, shorter length, or longer length of two structures.
  • 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
  • 2006/06/20: select 'A' if there is altLoc when reading PDB file.
  • 2005/10/19: the program was reformed so that the alignment results are not dependent on the specific compilers.
  • 2005/06/01: A bug of two-point superposition was fixed.
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