Difference between revisions of "Atomtype"

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(Explaining some dependencies in expert systems)
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The atom typing algorithm is based on a flexible [[PATTY]] expert  system. This assignment requires previously assigned [[Aromaticity]] and [[Hybridisation]] informations.
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The atom typing algorithm is based on a flexible [[PATTY]] expert  system ([[Article:bs93]]). This assignment requires previously assigned [[Aromaticity]] and [[Hybridisation]] informations. Some basic atom typing rules were e.g. published by ([[Article:ksfams96]])
 
==Data ([[PATTY]] expert system)==
 
==Data ([[PATTY]] expert system)==
 
* [http://cvs.sourceforge.net/viewcvs.py/openbabel/openbabel/data/atomtyp.txt?view=markup atomtyp.txt]
 
* [http://cvs.sourceforge.net/viewcvs.py/openbabel/openbabel/data/atomtyp.txt?view=markup atomtyp.txt]
==References==
 
@Article{bs93,
 
  author = {B. L. Bush and R. P. Sheridan},
 
  title = {{PATTY}: {A} {P}rogrammable {A}tom {T}yper and {L}anguage for {A}utomatic
 
          {C}lassification of {A}toms in {M}olecular {D}atabases.},
 
  journal = {J. Chem. Inf. Comput. Sci.},
 
  year = {1993},
 
  volume = {33},
 
  pages = {756-762},
 
}
 
 
@Article{ksfams96,
 
  author = {S. K. Kearsley and S. Sallamack and E. M. Fluder and J. D. Andose
 
            and R. T. Mosley and R. P. Sheridan},
 
  title = {{C}hemical {S}imilarity {U}sing {P}hysiochemical {P}roperty {D}escriptors},
 
  journal = {J. Chem. Inf. Comput. Sci.},
 
  year = {1996},
 
  volume = {36},
 
  pages = {118--127},
 
  abstract = {Similarity searches using topological descriptors have proved extremely
 
        useful in aiding large-scale screening. We describe alternative
 
        forms of the atom pair (Carhart et al. J. Chem. Inf. Comput. Sci.
 
        1985, 25,64-73.) and topological torsion (Nilakantan et al. J. Chem.
 
        Inf. Comput. Sci. 1987, 27,82-85.) descriptors that use physiochemical
 
        atom types. These types are based on binding property class, atomic
 
        log P contribution, and partial atomic charges. The new descriptors
 
        are meant to be more fuzzy than the original descriptors. We propose
 
        objective criteria for determining how effective one descriptor
 
        is versus another in selecting active compounds from large databases.
 
        Using these criteria, we run similarity searches over the Derwent
 
        Standard Drug File with ten typical druglike probes. The new descriptors
 
        are not as good as the original descriptors in selecting actives
 
        if one considers the average over all probes, but the new descriptors
 
        do better for several individual probes. Generally we find that
 
        whether one descriptor does better than another varies from probe
 
        to probe in a way almost impossible to predict a priori. Most importantly,
 
        we find that different descriptors typically select very different
 
        sets of actives. Thus it is advantageous to run similarity probes
 
        with several types of descriptors.},
 
  doi = {[http://dx.doi.org/10.1021/ci950274j 10.1021/ci950274j]}
 
}
 

Revision as of 11:43, 4 March 2006

The atom typing algorithm is based on a flexible PATTY expert system (Article:bs93). This assignment requires previously assigned Aromaticity and Hybridisation informations. Some basic atom typing rules were e.g. published by (Article:ksfams96)

Data (PATTY expert system)