Multiple Grid Arrangement on Glide

Introduction

Multiple Grid Arrangement is a novel deep conformational search method for grid-based protein-ligand docking software. This website provide the script of multiple grid arrangement used on Schrödinger Glide.

Download

xglide_mga.py (version 1.0, Last update: 28 Jan, 2016)

Usage

Installation

 $ cp xglide_mga.py $SCHRODINGER/mmshare-vXXXXX/python/common/

Run

 $ $SCHRODINGER/run $SCHRODINGER/mmshare-vXXXXX/python/common/xglide_mga.py inputfile.inp

Dataset

AstexDiverse.tar.gz (30.3 MB)

* Astex Diverse Dataset (85 complexes) converted Maestro files (.mae) used in the paper of Ban et al., 2016.

Sample input file

redocking example

### XGlide input file ###

RECEPTOR    1g9v.mae
LIGAND      1g9v_ligand.mae,REFPOSE

ALIGN       FALSE
PPREP                                             TRUE
GRIDGEN_GRID_CENTER                               SELF
GRIDGEN_OUTERBOX                                  30
GRIDGEN_RANDOM_SETTING                            TRUE
SITEMAP                                           TRUE
LIGPREP                                           TRUE
LIGPREP_EPIK                                      TRUE
DOCK_PRECISION                                    SP
DOCK_WRITE_XP_DESC                                FALSE
DOCK_POSE_OUTTYPE                                 poseviewer
NATIVEONLY                                        FALSE
DOCK_LIG_VSCALE                                   0.80
SKIP_DOCKING                                      FALSE
GENERATE_TOP_COMPLEXES                            1

cross-docking example

### XGlide input file ###

RECEPTOR    1g9v.mae
RECEPTOR    1gkc.mae
RECEPTOR    2bsm.mae

LIGAND      1g9v_ligand.mae
LIGAND      1gkc_ligand.mae
LIGAND      2bsm_ligand.mae

ALIGN       FALSE
PPREP                                             TRUE
GRIDGEN_GRID_CENTER                               SELF
GRIDGEN_OUTERBOX                                  30
GRIDGEN_RANDOM_SETTING                            TRUE
SITEMAP                                           TRUE
SITEMAP_MAXSITES                                  5
SITEMAP_FORCE                                     TRUE
LIGPREP                                           TRUE
LIGPREP_EPIK                                      TRUE
DOCK_PRECISION                                    SP
DOCK_WRITE_XP_DESC                                FALSE
DOCK_POSE_OUTTYPE                                 poseviewer
NATIVEONLY                                        FALSE
DOCK_LIG_VSCALE                                   0.80
SKIP_DOCKING                                      FALSE
GENERATE_TOP_COMPLEXES                            1

Performance

Figure: RMSD curve result of re-docking test using Astex diverse dataset.

Blue and green lines indicate percentage of complexes at each RMSD (Å) between ligands of native and predicted complexes in standard Glide (SP mode) and proposed method (multiple grid arrangement) on Glide SP mode, respectively. Note that percentages at 1.0 Å and 2.0 Å indicate docking accuracy.

License

The script on this web site have been generated by Schrödinger and by the authors. The script is provided free of charge. The script is provided "as is" without warranty of any kind, and may not be error free. Schrödinger and the authors of this script disclaim all warranties, express or implied, including warranties of merchantability and fitness for a paricular purpose. In no event shall Schrödinger or the authors of this script be liable for special, incidental or consequential damages of any kind.

The original xglide.py script can be download at Schrödinger script center.

Contact

ban [at] bi.c.titech.ac.jp (Tomohiro Ban, Tokyo Institute of Technology)

Reference

Tomohiro Ban, Masahito Ohue, Yutaka Akiyama. Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem, Computational Biology and Chemistry, 73: 139-146, 2018. doi: 10.1016/j.compbiolchem.2018.02.008. (open access)