Hint 2.30 Manual: Release Notes for HINT 2.35S

Release Notes for HINT 2.35S

  1. HINT 2.35S has been optimized to work with SYBYL 6.6+
    HINT was compiled:
    • Under Irix 6.5 on a R4400 SGI using the -mips3 compiler directive and the Sybyl 6.6 R5000 binary libraries for R5000+ processors
    (See the Installation instructions for more information.)

  2. An error has been discovered in the interaction matrix for classifying and setting the sign of interactions for Interaction Tables and Interaction Maps. This particular error was only a problem when interacting two species that were (both) partitioned with the "ALL" Hydrogens Option. Interactions between hydrophobic (apolar) hydrogens and polar heavey atoms were being misclassified and assigned the wrong sign. (They should be unfavorable hydrophobic-polar). We have fixed the error. It should be pointed out that we have generally recommended using ESSENTIAL hydrogen paritioning when perfori=ming interaction calculations, for several reasons: 1) apolar hydrogens are never explicitly located in experimental structures of biomacromolecules, so using their locations in sensitive distance-based calculations may be overextending the actual structure data; 2) the HINT parameterization for splitting, for example a methyl, into four separate atoms is uncertain, and 3) this would appear to add unneccessary complications to the calculation. A methyl-methyl interaction would become 16 separate calculations. We have added some text in the Theory section of the manual to more explicitly define the interaction matrix and its effect on HINT interaction calculations. (Through extensive calculations, Andrea Mozzarelli, Anna Marabotti, Pietro Cozzini, and Lara Balestreri of the University of Parma have located and characterized this problem.)

  3. We have revised the HINT partition dictionary for nucleic acid bases, particularly for RNA.

  4. The hintcells.spl script had errors. These have been corrected. (Thank you to David Demeter of Dow AgroSciences for pointing out this error.)

  5. Using some of the HINT functions with Sybyl NetBatch was not working due to a corrupted version of "hint_batch" being shipped with the previous release of HINT. This has been corrected. (Thank you to Douglas Sherman of Becton-Dickinson for discovering and reporting this problem.)

  6. NO2 was not being properly partitioned. This has been corrected. (Thanks to Yoshiaki Nakagawa of Kyoto University.)

  7. Previous versions of HINT will not operate after this end of this year due to a date rollover in the License Manager.