[Chimera-users] MatchMaker algorithm

[Elaine Meng]

Dear Liuqing Chen,
Matchmaker uses a unique approach involving both sequence and secondary structure information, first creating an alignment in 2D (along the sequence) which is then used for fitting in 3D. Choosing Needleman-Wunsch or Smith-Waterman only affects one part of the overall Matchmaker method: whether the 2D alignment step is done globally or locally.  So, it would not really make sense to substitute some other method for just that step.

Probably you really meant, in addition to Matchmaker, you would like SSM as an additional method of superimposing structures.  There are a large number of different methods, and we haven’t had the programmer resources to add others yet, or to connect to web services that provide them.  In the meanwhile, you could use this web server
<http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver>
… or several other superposition servers linked here
<http://www.rbvi.ucsf.edu/home/meng/grpmt/structalign.html>

Of the hundreds of different methods, you would have to try the experiment yourself to answer your question about whether the results are different.  I would guess that surely the results would be different but they might be extremely similar as well, depending on how “hard” your test cases are.  My longer list in the link above includes literature references, some of which include comparisons of methods.

Matchmaker has been popular and successful, so we haven’t felt much need for additional methods.  Besides Matchmaker, there are a few other approaches for superimposing structures in Chimera, as summarized here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 14, 2016, at 11:52 PM, 陈柳青 <519198561 at 163.com> wrote:

> Respected Sir/Madam
> The ucsf matchmaker algorithm is "Needleman-Wunsch" and "Smith-Waterman", but other program use SSM algorithm, such as ccp4mg, cuemol et al.,  can chimera add SSM algorithm?  and whether  these algorithm  will affect results differently?
> sincerely
> Liuqing chen