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| − | The atom typing algorithm is based on a flexible [[PATTY]] expert system. | + | 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://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/data/atomtyp.txt?view=markup atomtyp.txt] |
| − | ==References==
| + | * [http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/data/types.txt?view=markup types.txt] |
| − | @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]}
| + | |
| − | }
| + | |
