DOCK 6.5 This is a release of the version applied in references [1] and [2]. NEW IN DOCK 6.5 ###New Anchor Controls### Now one can choose the anchor used during growth. In addition, one can limit the max number of anchors used during multiple-anchor docking. The new input parameters for this anchor selection are listed below. ###New Scoring Function### Descriptor Score is a newly introduced scoring function, which reports van der Waals and Coulombic energies, hydrogen bonds, and per-residue energy decomposition comparisons with a reference molecule. For more information on Descriptor Score see ref. [1]. ###Amber Score Improvements### The cofactors library, leaprc.dock.cofactors, and the ions library, leaprc.dock.ions, have grown substantially. These offer automatic support for simple treatments of common cofactors and ions. ###PB/SA Score Improvements### PB/SA score has undergone some generalizations and efficiency improvements that make docking, as opposed to rescoring, more tractable for nontrivial systems. ###Miscellaneous### If heavy atom RMSD calculation is activated in program DOCK then the RMSDs are now also emitted in the DOCK standard output file as well as the structural output files. The label for RMSDs in output files has changed; see below. In program grid, atom valence violations detected during van der Waals label assignments now emit warning messages instead of causing fatal terminations. Such warnings should be thoroughly investigated since they are usually caused by inadequate preparation. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 DOCK runs with the second run specifying amber_score as the primary_score. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUG FIXES Some bug reports have not yet been processed, but several important bugs have been fixed since the last release. For DOCK: Incorrect Amber score input filenames for neutralized, solvated RNA complexes. This caused duplicated filenames and loss of information. For sphere_selector: Inadequate error checking in sphere file reading. This bug was only exercised when the sphere file had size zero; in that case an infinite loop occurred. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ INPUT PARAMETER CHANGES AND THEIR DEFAULT VALUES Added: For Anchor selection ( Anchor & Grow Parameters) user_specified_anchor [no] (yes no): atom_in_anchor [C1,1] (): limit_max_anchors [no] (yes no): max_anchor_num [1] (): For descriptor Score: descriptor_score_primary [no] (yes no): descriptor_score_secondary [no] (yes no): desc_use_footprint_reference_mol2 [no] (yes no): desc_footprint_reference_mol2_filename [ligand_footprint.mol2] (): desc_use_footprint_reference_txt [no] (yes no): desc_footprint_reference_txt_filename [ligand_footprint.txt] (): desc_foot_compare_type [r] (r d): desc_normalize_foot [yes] (yes no): desc_foot_comp_all_residue [yes] (yes no): desc_choose_foot_range_type [specify_range] (specify_range threshold): desc_range [20-40,60-80] (): desc_vdw_threshold [1] (): desc_es_threshold [1] (): desc_hb_threshold [0.5] (): desc_use_remainder [yes] (yes no): desc_score_rec_filename [receptor.mol2] (): desc_score_att_exp [6] (): desc_score_rep_exp [12] (): desc_score_rep_rad_scale [1] (): desc_use_distance_dependent_dielectric [yes] (yes no): desc_score_dielectric [4.0] (): desc_score_vdw_scale [1] (): desc_score_es_scale [1] (): desc_score_hb_scale [0] (): desc_score_internal_scale [0] (): desc_score_fp_vwd_scale [0] (): desc_score_fp_es_scale [0] (): desc_score_fp_hb_scale [0] (): Removed: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FILE FORMAT CHANGES For DOCK: The label for RMSDs in output files has changed from '#HEAVY ATM RMSD' to '########## HA_RMSD'. New file type for reading in a reference footprint. Format is as follows: #################################### ### Reference FP #################################### resname resid vdw_ref es_ref hb_ref GLY1 1 -0.000045 -0.000061 0 GLU2 2 -0.000226 0.000032 0 ALA3 3 -0.000174 -0.000093 0 PRO4 4 -0.000266 0.000186 0 ASN5 5 -0.001091 0.000538 0 GLN6 6 -0.000612 0.000165 0 ALA7 7 -0.001325 -0.000591 0 LEU8 8 -0.002368 0.000552 0 LEU9 9 -0.007224 0.000388 0 ARG10 10 -0.007143 -0.008906 0 ILE11 11 -0.004132 0.000615 0 LEU12 12 -0.012233 -0.000404 0 LYS13 13 -0.002511 -0.003366 0 GLU14 14 -0.004349 0.005031 0 THR15 15 -0.001461 0.000304 0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ REFERENCES 1. 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 (10), 2273.2289. doi: 10.1002/jcc.21814 PMID: 21541962 2. Docking and Scoring: A Review of Docking Programs, a Symposium at the March 2011 ACS Meeting. http://abstracts.acs.org/chem/241nm/program/divisionindex.php?act=presentations&val=Docking+and+Scoring%3A+A+Review+of+Docking+Programs&ses=Docking+and+Scoring%3A+A+Review+of+Docking+Programs&prog=54110