fragment-based-docking-scoring/main

Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring

Inputs

ID	Name	Description	Type
All fragments (SDF)	All fragments (SDF)	Fragments in SDF format	File
Candidate compounds (SMILES)	Candidate compounds (SMILES)	List of compounds for docking in SMILES format	File
Collection size for docking	Collection size for docking	Parameter for parallelization of docking	int
MOL)	Fragment for SuCOS scoring (SDF/MOL)	SDF or MOL file with the single fragment for SuCOS scoring	File
Number of poses	Number of poses	Number of docking poses to generate per input compound	int
Receptor (PDB)	Receptor (PDB)	PDB file for the receptor protein	File
SuCOS threshold	SuCOS threshold	Value between 0 and 1. All poses with a SuCOS score lower than this value will be filtered out.	float

Steps

ID	Name	Description
7	Compound conversion	toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0
8	Create Frankenstein ligand	toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0
9	Compose text parameter value	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
10	Enumerate changes	toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0
11	rDock cavity definition	toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/2013.1.1_148c5bd1+galaxy0
12	Compound conversion	toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0
13	Split file	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
14	rDock docking	toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/2013.1.1_148c5bd1+galaxy0
15	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
16	Score docked poses using SuCOS	toolshed.g2.bx.psu.edu/repos/bgruening/sucos_docking_scoring/sucos_docking_scoring/2020.03.4+galaxy1
17	rDock docking	toolshed.g2.bx.psu.edu/repos/bgruening/rdock_sort_filter/rdock_sort_filter/2013.1-0+galaxy0

Outputs

ID	Name	Description	Type
Docking poses	Docking poses	n/a	File
Scored and filtered poses	Scored and filtered poses	n/a	File

Version History

Updated to v0.1.4

Frozen v0.1.4 062e4e0

Updated to v0.1.2

Open master e42d116

Updated to v0.1.1

Frozen master db0c104

Added/updated 9 files

Frozen master 8a02b10

fragment-based-docking-scoring/main
v0.1.4 (latest)

v0.1.4 (latest)

v0.1.2

v0.1.1

v0.1 (earliest)