[Dock-fans] Conserved Interactions

Terry Lang terry at cgl.ucsf.edu
Thu May 11 13:40:11 PDT 2006

Dear Peng,

       This can be accomplished in one of two ways.  See below for more 
details on the two options.  For more information on how to implement 
these options in a DOCK run, see the DOCK 4 manual at 


*Critical Points *

The critical_points feature is used to focus the orientation search into 
a subsite of the receptor active site (DesJarlais, et al. J. 
Comput-Aided Molec. Design. 1994 and Miller, et al J. Comput. Aided Mol. 
Design. 1994). For example, identifying molecules that interact with the 
catalytic residues might be of chief interest. Any number of points may 
be identified as critical, and any number of groupings of these points 
may be identified. An alternative to using critical points is to discard 
all site points that are some distance away from the subsite of 
interest, while retaining enough site points to define unique ligand 
orientations. This feature can be highly effective at reducing matching 
by five-fold or more. It is particularly useful to also assign chemical 
labels to the critical points to further focus sampling.

*Chemical Matching*

The chemical_matching feature is used to incorporate information about 
the chemical complementarity of a ligand orientation into the matching 
process. In this feature, chemical labels are assigned to site points 
and ligand atoms (Kuhl, et al. J. Comput. Chem. 1984). The site point 
labels are based on the local receptor environment. The ligand atom 
labels are based on user-adjustable chemical functionality rules. These 
labeling rules are identified with the chemical_defn_file parameter and 
reside in an editable file. A node in a match will produce an 
unfavorable interaction if the atom and site point components have 
labels which violate a chemical match rule. The chemical matching rules 
are identified with the chemical_match_file parameter and reside in an 
editable file. If a match will produce unfavorable interactions, then 
the match is discarded. The speed-up from this technique depends how 
extensively site points have been labeled and the stringency of the 
match rules, but an improvement of two-fold or more can be expected.

LIU,PENG wrote:

> Hi all,
>  I got a question: How can you constrain groups of the ligand so that 
> they can maintain, say, hydrogen-bonding interactions with certain 
> residues of the receptor during the docking process?
> Thanks!
> Peng
> -- 
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P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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