FILTER 2.0.1 (January 2007)

This release is a broad-sweeping bug fix release with a dramatically improved introduction in the documentation. It includes many simple and complex bug fixes including; conceptual clarifications of several algorithms, fixes and improvements to the data representation, several advances in the pKa model, and significantly more documentation. While this is only a bug-fix release, it represents a significant step-forward in the refinement of the product. We hope you find it suits your needs.

New features

  • Added three additional filters that are designed around the best-selling prescription drugs
  • Predicted aggregator QSAR model introduced to further enhance aggregator recognition capability
  • Implemented an algorithm for “total functional group count” that takes account of all functional groups rather than only those included in the filter patterns
  • Added -tableFlag parameter to mark all failure values in the table file with an asterisk
  • Extended the unique flag to allow values of “true”, “false” or a filename used to pre-load a file of uniques
  • Added pKa for phenol groups with significant electron withdrawing groups

Bug fixes

  • Fixed two bugs in the algorithm for recognizing hydrogen-bond donors and acceptors
  • Abbott Bioavailability Score corrected to be reported as a probability
  • Aggregator function augmented to include more than 250 additional known aggregators
  • XLogP and LogS corrected to always examine the hypervalent form of molecules (as are used in the training set)
  • Improved data reporting and filter control for the pharmacokinetic properties
  • Fixed category reporting for solubility calculation
  • Changed the default TPSA calculation to ignore rather than include P and S surface area
  • Renamed and clarified aliphatic_group filter to “maximum connected non-ring atoms”
  • Fixed typos in names beta_carbonyl_quat_nitrogen and t_butoxycarbonyl_tBOC
  • Updated chloramidine filter name to the more common imidoyl_chloride
  • Fixed error in beta_azo_carbonyl pattern
  • Made patterns for cytochalasin, monensin, squalestatin and saponin more specific
  • Clarified the exclusion patterns for acyclic_NCN and SCN2
  • Dramatically improved the specificity and range of the michael_acceptor pattern
  • Fixed error in alkyl_halide pattern that limited it to bromine and iodine
  • Fixed multiple patterns that matched their function group multiple times because of symmetry
  • Limited enamine definition to exclude exceedingly delocalized instances
  • Fix t_butyl_ether pattern to avoid matching t_butyl_alcohols
  • Removed dependence of rigid bond count upon implicit or explicit hydrogens
  • Cleaned-up table data for the select parameter
  • Corrected problem that MIN_HALIDE_FRACTION and ALLOWED_ELEMENTS could not properly be removed from the filter file
  • Fixed bug so NEWRULE lines with tailing white space are not ignored
  • Fixed crash bug that occurred when a filter file was specified that was not a valid file
  • Improved pKa value for barbiturate-like compounds
  • Clarified alpha-acyl carbon deprotonation
  • Removed 1,2,3 triazole pKa rule
  • Clarified tertiary amine rule
  • Improved efficiency for applying pKa rules to multi-conformer molecules