DOCK 6.7 This is a release of the version applied in reference [1]. NEW IN DOCK 6.7 ###Input Parameter Default Values### Based on a performance assessment [1] using large data sets containing systems with diverse structure and chemistry and employing multiple metrics, which were pose reproduction, cross-docking, and database enrichment, the default values for several input parameters have been updated: max_orientations 500 -> 1000 use_internal_energy no -> yes pruning_max_orients 100 -> 1000 pruning_conformer_score_cutoff 25.0 -> 100.0 bump_filter yes -> no simplex_grow_max_iterations 20 -> 500 In order to make the footprint scores [2-3] easily accessible and user friendly the standard euclidean comparison is recommended. Thus, the default values for several input parameters have been updated: desc_foot_compare_type r -> d desc_normalize_foot yes -> no multigrid_score_use_euc no -> yes multigrid_score_use_norm_euc yes -> no ###Miscellaneous### Incremental improvements in documentation, installation, and testing. As of version 6.3 DOCK officially stopped supporting SGI platforms because the developers no longer have access to SGI machines. However, user interest has continued, and the sgi configuration files have been updated based on feedback. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DEPRECATED FEATURES 1. For a variety of reasons still under active development, amber_score cannot effectively be used as a secondary_score. This function was temporarily deprecated in 6.1, and using input parameter amber_score_secondary causes program termination. The recommended protocol is to perform two sequential DOCK runs where the output ligand poses from the first run are rescored specifying amber_score as the primary_score in the second run. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUG FIXES Some bug reports have not yet been processed, but several important bugs have been fixed since the last release. For multigrid_fp_gen.py: Bond information is not written to the individual-residue-mol2 files that are used to make the individual-residue-grids; the @BOND sections are empty. This caused the same ligand pose scored on a correct grid to differ in VDW energy by as much as ~10% compared to a faulty grid. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INPUT PARAMETER CHANGES AND THEIR DEFAULT VALUES Changed: bump_filter [no] (yes, no) desc_foot_compare_type [d] (r d) desc_normalize_foot [no] (yes no) max_orientations [1000] (int) multigrid_score_use_euc [yes] (yes no) multigrid_score_use_norm_euc [no] (yes no) pruning_conformer_score_cutoff [100.0] (float) pruning_max_orients [1000] (int) simplex_grow_max_iterations [500] (int) use_internal_energy [yes] (yes no) Added: Removed: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FILE FORMAT CHANGES None. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ REFERENCES 1. Allen, W. J.; Balius, T. E.; Mukherjee, S.; Brozell, S. R.; Moustakas, D. T.; Lang, P. T.; Case, D. A.; Kuntz, I. D.; Rizzo, R. C. DOCK 6: Impact of New Features and Current Docking Performance. J. Comput. Chem. 2014, Submitted. 2. Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method Using Molecular Footprint Comparisons. J. Comput. Chem. 2011, 32, 2273-2289. 3. Balius, T. E.; Allen, W. J.; Mukherjee, S.; Rizzo, R. C. Grid-Based Molecular Footprint Comparison Method for Docking and De Novo Design: Application to HIVgp41. J. Comput. Chem. 2013, 34, 1226-1240.