[Chimera-users] Enquiry: Match Maker

Elaine Meng meng at cgl.ucsf.edu
Tue May 6 10:46:50 PDT 2014

Hi Anna,
My first impression is that MatchMaker is not the appropriate tool for such a study.  You may instead wish to use one of the many "3D motif"-related software tools.   There may be dozens of such resources, but to name a few:

LabelHash server <http://labelhash.kavrakilab.org/>
PINTS server <http://www.russelllab.org/cgi-bin/tools/pints.pl>
funClust server <http://pdbfun.uniroma2.it/funclust/index2.py>
pdbFun server <http://pdbfun.uniroma2.it/>

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

On May 6, 2014, at 2:59 AM, Anna Hernandez <annahernandezduran at gmail.com> wrote:

> Hi,
> I have a question regarding structural alignments with Match Maker.
> I would like to know if there is any way to obtain a list of all possible alignment solutions (or a subset) tested by Match Maker, instead of only the "best" one, so that I can further assess the different options manually.
> Specifically I am trying to find an homologous substructure/motif from my template structure within a query structure. The pattern to be searched is rather small as compared to the whole protein and it can be aligned in multiple positions. I would like to assess each of the possibilities more carefully based on the biological knowledge of the protein.
> Thank you in advance.
> Best wishes,
> Anna Hernandez

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