From 178d52b31ca249a406626308a68b3774006c697b Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Tue, 25 Mar 2025 13:24:19 +0530 Subject: [PATCH 01/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index ab86582c7bde94..ee532efe3eeb4b 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -246,6 +246,7 @@ Further, docking requires the coordinates of a binding site to be defined. Effec > > 1. {% tool [Prepare receptor](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Select a PDB file"*: 'Protein' PDB file. +> - Rename to 'Prepared receptor' > 2. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Compound library' file. > - {% icon param-file %} *"Output format"*: `SDF` @@ -298,8 +299,8 @@ Now that the protein and the ligand library have been correctly prepared and for > Perform docking > -> 1. {% tool [Docking](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0) %} with the following parameters: -> - {% icon param-file %} *"Receptor"*: 'Protein PDBQT' file. +> 1. {% tool [VINA Docking](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0) %} with the following parameters: +> - {% icon param-file %} *"Receptor"*: 'Protein receptor' file. > - {% icon param-file %} *"Ligands"*: 'Prepared ligands' file. > - {% icon param-file %} *"Specify pH value for ligand protonation"*: `7.4` > - {% icon param-file %} *"Specify parameters"*: 'Upload a config file to specify parameters' From 34c8e91dd6c0d3403ce55c933260e324d250c2ed Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Tue, 25 Mar 2025 17:10:07 +0530 Subject: [PATCH 02/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index ee532efe3eeb4b..4071eed9bb708f 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -299,7 +299,7 @@ Now that the protein and the ligand library have been correctly prepared and for > Perform docking > -> 1. {% tool [VINA Docking](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0) %} with the following parameters: +> 1. {% tool [VINA Docking](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Receptor"*: 'Protein receptor' file. > - {% icon param-file %} *"Ligands"*: 'Prepared ligands' file. > - {% icon param-file %} *"Specify pH value for ligand protonation"*: `7.4` From 0ed9b88e025301ea5b551875aa4a0418f9b79337 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 26 Mar 2025 11:41:49 +0530 Subject: [PATCH 03/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 4071eed9bb708f..13d1ad52806626 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -247,9 +247,9 @@ Further, docking requires the coordinates of a binding site to be defined. Effec > 1. {% tool [Prepare receptor](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Select a PDB file"*: 'Protein' PDB file. > - Rename to 'Prepared receptor' -> 2. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0) %} with the following parameters: +> 2. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Compound library' file. -> - {% icon param-file %} *"Output format"*: `SDF` +> - {% icon param-file %} *"Output format"*: `MDL MOL format (sdf,mol)` > - {% icon param-file %} *"Generate 3D coordinates"*: `Yes` > - {% icon param-file %} *"Add hydrogens appropriate for pH"*: `7.4` > - Leave all other options unchanged. From 90a77b9b7fb687c510b2929684a59757119031fa Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 26 Mar 2025 14:17:31 +0530 Subject: [PATCH 04/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 13d1ad52806626..8de0586f88ba41 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -400,7 +400,7 @@ From our collection of SD-files, we first extract all stored values into tabular > 2. {% tool [Collapse Collection](toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2) %} with the following parameters: > - {% icon param-file %} *"Collection of files to collapse into single dataset"*: Collection of tabular files generated by the previous step. > - {% icon param-file %} *"Keep one header line"*: `Yes` -> - {% icon param-file %} *"Append File name"*: `No` +> - {% icon param-file %} *"Prepend File name"*: `No` > > {% snippet faqs/galaxy/tools_select_collection.md datatype="datatypes" %} > From 0336d9b5184db738adb6dba49b9d233f49470f90 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 26 Mar 2025 17:47:34 +0530 Subject: [PATCH 05/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 8de0586f88ba41..48c8cd3b37f90f 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -82,7 +82,7 @@ You can view the contents of the downloaded PDB file by pressing the 'View data' > Separate protein and ligand > -> 1. {% tool [Search in textfiles (grep)](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1) %} with the following parameters: +> 1. {% tool [Search in textfiles (grep)](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Select lines from"*: Downloaded PDB file 'Hsp90 structure' > - {% icon param-file %} *"that"*: `Don't match` > - {% icon param-file %} *"Regular Expression"*: `HETATM` @@ -90,7 +90,7 @@ You can view the contents of the downloaded PDB file by pressing the 'View data' > - Rename the dataset **'Protein (PDB)'**. > > The result is a file with all non-protein (`HETATM`) atoms removed. -> 2. {% tool [Search in textfiles (grep)](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1) %} with the following parameters. Here, we use grep again to produce a file with only non-protein atoms. +> 2. {% tool [Search in textfiles (grep)](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy0) %} with the following parameters. Here, we use grep again to produce a file with only non-protein atoms. > - {% icon param-file %} *"Select lines from"*: Downloaded PDB file 'Hsp90 structure' > - {% icon param-file %} *"that"*: `Match` > - {% icon param-file %} *"Regular Expression"*: `CT5` (the name of the ligand in the PDB file) From d63a1f7323d38cd8612178df6f4d5dd3e6f30915 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 26 Mar 2025 18:01:05 +0530 Subject: [PATCH 06/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 48c8cd3b37f90f..1d9bd7f4ac41f8 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -98,7 +98,7 @@ You can view the contents of the downloaded PDB file by pressing the 'View data' > - Rename the dataset **'Ligand (PDB)'**. > > This produces a file which only contains ligand atoms. -> 3. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0) %} with the following parameters: +> 3. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: Ligand PDB file created in step 2. > - {% icon param-file %} *"Output format"*: `MDL MOL format (sdf, mol)` > - {% icon param-file %} *"Add hydrogens appropriate for pH"*: `7.4` @@ -128,7 +128,7 @@ We will generate our compound library by searching ChEMBL for compounds which ha > Generate compound library > -> 1. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0) %} with the following parameters: +> 1. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Ligand' PDB file > - {% icon param-file %} *"Output format"*: `SMILES format (SMI)` > - Leave all other options as default. @@ -254,7 +254,7 @@ Further, docking requires the coordinates of a binding site to be defined. Effec > - {% icon param-file %} *"Add hydrogens appropriate for pH"*: `7.4` > - Leave all other options unchanged. > - Rename to 'Prepared ligands' -> 3. {% tool [Calculate the box parameters for an AutoDock Vina job](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.4+galaxy0) %} with the following parameters: +> 3. {% tool [Calculate the box parameters using RDKit] for an AutoDock Vina job from a ligand or pocket input file (confounding box)(toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.5+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Input ligand or pocket"*: `Ligand (MOL)` file. > - {% icon param-file %} *"x-axis buffer"*: `5` > - {% icon param-file %} *"y-axis buffer"*: `5` @@ -299,7 +299,7 @@ Now that the protein and the ligand library have been correctly prepared and for > Perform docking > -> 1. {% tool [VINA Docking](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0) %} with the following parameters: +> 1. {% tool [VINA Docking] tool to perform protein-ligand docking with Autodock Vina (toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Receptor"*: 'Protein receptor' file. > - {% icon param-file %} *"Ligands"*: 'Prepared ligands' file. > - {% icon param-file %} *"Specify pH value for ligand protonation"*: `7.4` From 847166dc0656e8139d2729c50f92a522648fed42 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Wed, 26 Mar 2025 18:35:55 +0530 Subject: [PATCH 07/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 1d9bd7f4ac41f8..3480db671b0ee7 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -98,7 +98,7 @@ You can view the contents of the downloaded PDB file by pressing the 'View data' > - Rename the dataset **'Ligand (PDB)'**. > > This produces a file which only contains ligand atoms. -> 3. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 3. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: Ligand PDB file created in step 2. > - {% icon param-file %} *"Output format"*: `MDL MOL format (sdf, mol)` > - {% icon param-file %} *"Add hydrogens appropriate for pH"*: `7.4` @@ -128,7 +128,7 @@ We will generate our compound library by searching ChEMBL for compounds which ha > Generate compound library > -> 1. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 1. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Ligand' PDB file > - {% icon param-file %} *"Output format"*: `SMILES format (SMI)` > - Leave all other options as default. @@ -247,7 +247,7 @@ Further, docking requires the coordinates of a binding site to be defined. Effec > 1. {% tool [Prepare receptor](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Select a PDB file"*: 'Protein' PDB file. > - Rename to 'Prepared receptor' -> 2. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 2. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Compound library' file. > - {% icon param-file %} *"Output format"*: `MDL MOL format (sdf,mol)` > - {% icon param-file %} *"Generate 3D coordinates"*: `Yes` @@ -322,7 +322,7 @@ It can be useful to visualize the compounds generated. There is a tool available > Visualization of chemical structures > -> 1. {% tool [Visualisation](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0) %} with the following parameters: +> 1. {% tool [Visualisation](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: Compound library > - {% icon param-file %} *"Embed molecule as CML"*: `No` > - {% icon param-file %} *"Draw all carbon atoms"*: `No` @@ -344,15 +344,15 @@ In this step, we will group similar molecules together. A key tool in cheminform Before clustering, let's label each compound. To do so add a second column to the SMILES compound library containing a label for each molecule. The ```Ligand SMILES``` file is also labelled something like ```/data/dnb02/galaxy_db/files/010/406/dataset_10406067.dat``` (the exact name will vary) and we would like to give it a more useful name. When labelling is complete, we can concatenate (join together) the library file with the original SMILES file for the ligand from the PDB file. > Calculate molecular fingerprints -> 1. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3) %} with the following parameters: +> 1. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0) %} with the following parameters: > - {% icon param-file %} *"File to process"*: `Ligand SMILES`. > - {% icon param-file %} *"Find pattern"*: add the current label of the SMILES here. You can find it by clicking the 'view' button next to the `Ligand SMILES` dataset - it will look something like `/data/dnb02/galaxy_db/files/010/406/dataset_10406067.dat`. > - {% icon param-file %} *"Replace with"*: `ligand` -> 2. {% tool [Concatenate datasets](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1) %} with the following parameters: +> 2. {% tool [Concatenate datasets] tail-to-head (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/1.0.0) %} with the following parameters: > - {% icon param-file %} *"Datasets to concatenate"*: Output of the previous step. > - Click on **Insert Dataset** and in the new selection box which appears, select 'Compound library'. > - Run the step and rename the output dataset 'Labelled compound library'. -> 3. {% tool [Molecule to fingerprint](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5) %} with the following parameters: +> 3. {% tool [Molecule to fingerprint] conversion to several different fingerprint formats (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5) %} with the following parameters: > - {% icon param-file %} *"Molecule file"*: 'Labelled compound library' file. > - {% icon param-file %} *"Type of fingerprint"*: `Open Babel FP2 fingerprints` > - Rename to 'Fingerprints'. @@ -363,10 +363,10 @@ Taylor-Butina clustering ({% cite Butina1999 %}) provides a classification of t ![Image showing a Fingerprinting System]({% link topics/computational-chemistry/images/fingerprints.png %} "A simple fingerprinting system. Each 1 or 0 in the bitstring corresponds to the presence or absence of a particular feature in the molecule. In this case, the presence of phenyl, amine and carboxylic acid groups are encoded.") > Cluster molecules using molecular fingerprints -> 1. {% tool [Taylor-Butina clustering](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5) %} with the following parameters: +> 1. {% tool [Taylor-Butina clustering] of molecular fingerprints (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5) %} with the following parameters: > - {% icon param-file %} *"Fingerprint dataset"*: 'Fingerprints' file. > - {% icon param-file %} *"threshold"*: `0.8` -> 2. {% tool [NxN clustering](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1) %} with the following parameters: +> 2. {% tool [NxN clustering] of molecular fingerprints (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1) %} with the following parameters: > - {% icon param-file %} *"Fingerprint dataset"*: 'Fingerprints' file. > - {% icon param-file %} *"threshold"*: `0.0` > - {% icon param-file %} *"Format of the resulting picture"*: `SVG` @@ -391,20 +391,20 @@ From our collection of SD-files, we first extract all stored values into tabular > Process SD-files > -> 1. {% tool [Extract values from an SD-file](toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0) %} with the following parameters: +> 1. {% tool [Extract values from an SD-file] into a tabular file using RDKit (toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Input SD-file"*: Collection of SD-files generated by the docking step. (Remember to select the 'collection' icon!) > - {% icon param-file %} *"Include the property name as header"*: `Yes` > - {% icon param-file %} *"Include SMILES as column in output"*: `Yes` > - {% icon param-file %} *"Include molecule name as column in output"*: `Yes` > - Leave all other paramters unchanged. -> 2. {% tool [Collapse Collection](toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2) %} with the following parameters: +> 2. {% tool [Collapse Collection] into single dataset in order of the collection (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0) %} with the following parameters: > - {% icon param-file %} *"Collection of files to collapse into single dataset"*: Collection of tabular files generated by the previous step. > - {% icon param-file %} *"Keep one header line"*: `Yes` > - {% icon param-file %} *"Prepend File name"*: `No` > > {% snippet faqs/galaxy/tools_select_collection.md datatype="datatypes" %} > -> 3. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0) %} with the following parameters: +> 3. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: > - {% icon param-file %} *"Molecular input file"*: choose one of the SD-files from the collection generated by the docking step. > - {% icon param-file %} *"Output format"*: `Protein Data Bank format (pdb)` > - {% icon param-file %} *"Split multi-molecule files into a collection"*: `Yes` From 7204014121c582d3c8339970ac1f908efe1f7c82 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 28 Mar 2025 21:47:58 +0530 Subject: [PATCH 08/20] Update tutorial.md --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 3480db671b0ee7..7cebd1b6a2f24e 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -316,7 +316,7 @@ The ChemicalToolbox contains a large number of cheminformatics tools. This secti (This section can also be completed while waiting for the docking, which can take some time to complete.) -### Visualization +## Visualization It can be useful to visualize the compounds generated. There is a tool available for this in Galaxy based on OpenBabel. From 6584a374f6bbe3a247ae2891853ed34e151eb4e3 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Sat, 29 Mar 2025 14:58:09 +0530 Subject: [PATCH 09/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 7cebd1b6a2f24e..7cc671e85667b9 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -397,7 +397,7 @@ From our collection of SD-files, we first extract all stored values into tabular > - {% icon param-file %} *"Include SMILES as column in output"*: `Yes` > - {% icon param-file %} *"Include molecule name as column in output"*: `Yes` > - Leave all other paramters unchanged. -> 2. {% tool [Collapse Collection] into single dataset in order of the collection (toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0) %} with the following parameters: +> 2. {% tool [Collapse Collection](toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0) %} into single dataset in order of the collection with the following parameters: > - {% icon param-file %} *"Collection of files to collapse into single dataset"*: Collection of tabular files generated by the previous step. > - {% icon param-file %} *"Keep one header line"*: `Yes` > - {% icon param-file %} *"Prepend File name"*: `No` From bcd74e52f6f978fb161219258557385241abfc63 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Sat, 29 Mar 2025 14:58:19 +0530 Subject: [PATCH 10/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 7cc671e85667b9..c885d3dd783879 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -391,7 +391,7 @@ From our collection of SD-files, we first extract all stored values into tabular > Process SD-files > -> 1. {% tool [Extract values from an SD-file] into a tabular file using RDKit (toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0) %} with the following parameters: +> 1. {% tool [Extract values from an SD-file](toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab/2020.03.4+galaxy0) %} into a tabular file using RDKit with the following parameters: > - {% icon param-file %} *"Input SD-file"*: Collection of SD-files generated by the docking step. (Remember to select the 'collection' icon!) > - {% icon param-file %} *"Include the property name as header"*: `Yes` > - {% icon param-file %} *"Include SMILES as column in output"*: `Yes` From 57b042b97101685c27c82b1301635b3856301b32 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:44:21 +0530 Subject: [PATCH 11/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index c885d3dd783879..b51f17a54f4cbf 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -128,7 +128,7 @@ We will generate our compound library by searching ChEMBL for compounds which ha > Generate compound library > -> 1. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 1. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} - interconvert between various chemistry and molecular modeling data files with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Ligand' PDB file > - {% icon param-file %} *"Output format"*: `SMILES format (SMI)` > - Leave all other options as default. From 966367c51d61e0bf97fd2cfdf0f29a99ee7916b4 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:44:47 +0530 Subject: [PATCH 12/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index b51f17a54f4cbf..b5e4802058e887 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -98,7 +98,7 @@ You can view the contents of the downloaded PDB file by pressing the 'View data' > - Rename the dataset **'Ligand (PDB)'**. > > This produces a file which only contains ligand atoms. -> 3. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 3. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} - interconvert between various chemistry and molecular modeling data files with the following parameters: > - {% icon param-file %} *"Molecular input file"*: Ligand PDB file created in step 2. > - {% icon param-file %} *"Output format"*: `MDL MOL format (sdf, mol)` > - {% icon param-file %} *"Add hydrogens appropriate for pH"*: `7.4` From f21e311924c46a35d00de5eb8f655e3fa82190b0 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:44:59 +0530 Subject: [PATCH 13/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index b5e4802058e887..822817372954ad 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -254,7 +254,7 @@ Further, docking requires the coordinates of a binding site to be defined. Effec > - {% icon param-file %} *"Add hydrogens appropriate for pH"*: `7.4` > - Leave all other options unchanged. > - Rename to 'Prepared ligands' -> 3. {% tool [Calculate the box parameters using RDKit] for an AutoDock Vina job from a ligand or pocket input file (confounding box)(toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.5+galaxy0) %} with the following parameters: +> 3. {% tool [Calculate the box parameters using RDKit](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box/2021.03.5+galaxy0) %} for an AutoDock Vina job from a ligand or pocket input file (confounding box) with the following parameters: > - {% icon param-file %} *"Input ligand or pocket"*: `Ligand (MOL)` file. > - {% icon param-file %} *"x-axis buffer"*: `5` > - {% icon param-file %} *"y-axis buffer"*: `5` From 51369de6d21bc2ce6eac6915692aa0a9febdc22a Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:45:41 +0530 Subject: [PATCH 14/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 822817372954ad..0c70fd080a5b66 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -299,7 +299,7 @@ Now that the protein and the ligand library have been correctly prepared and for > Perform docking > -> 1. {% tool [VINA Docking] tool to perform protein-ligand docking with Autodock Vina (toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0) %} with the following parameters: +> 1. {% tool [VINA Docking](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0) %} tool to perform protein-ligand docking with Autodock Vina with the following parameters: > - {% icon param-file %} *"Receptor"*: 'Protein receptor' file. > - {% icon param-file %} *"Ligands"*: 'Prepared ligands' file. > - {% icon param-file %} *"Specify pH value for ligand protonation"*: `7.4` From 15c60cca79c3cffe31e09ddc58eca6fa6d37ba10 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:46:04 +0530 Subject: [PATCH 15/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 0c70fd080a5b66..6a30bb5f3ca1f0 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -352,7 +352,7 @@ Before clustering, let's label each compound. To do so add a second column to th > - {% icon param-file %} *"Datasets to concatenate"*: Output of the previous step. > - Click on **Insert Dataset** and in the new selection box which appears, select 'Compound library'. > - Run the step and rename the output dataset 'Labelled compound library'. -> 3. {% tool [Molecule to fingerprint] conversion to several different fingerprint formats (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5) %} with the following parameters: +> 3. {% tool [Molecule to fingerprint](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/1.5) %} conversion to several different fingerprint formats with the following parameters: > - {% icon param-file %} *"Molecule file"*: 'Labelled compound library' file. > - {% icon param-file %} *"Type of fingerprint"*: `Open Babel FP2 fingerprints` > - Rename to 'Fingerprints'. From c46d43135e316e629deb7989cf83d1446fe6731f Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:46:14 +0530 Subject: [PATCH 16/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 6a30bb5f3ca1f0..7d9c3fef73f583 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -363,7 +363,7 @@ Taylor-Butina clustering ({% cite Butina1999 %}) provides a classification of t ![Image showing a Fingerprinting System]({% link topics/computational-chemistry/images/fingerprints.png %} "A simple fingerprinting system. Each 1 or 0 in the bitstring corresponds to the presence or absence of a particular feature in the molecule. In this case, the presence of phenyl, amine and carboxylic acid groups are encoded.") > Cluster molecules using molecular fingerprints -> 1. {% tool [Taylor-Butina clustering] of molecular fingerprints (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5) %} with the following parameters: +> 1. {% tool [Taylor-Butina clustering](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5) %} of molecular fingerprints with the following parameters: > - {% icon param-file %} *"Fingerprint dataset"*: 'Fingerprints' file. > - {% icon param-file %} *"threshold"*: `0.8` > 2. {% tool [NxN clustering] of molecular fingerprints (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1) %} with the following parameters: From 8a94925695c408da4cc0cdf5796a196ab8013c9f Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:46:59 +0530 Subject: [PATCH 17/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 7d9c3fef73f583..fd0fbd88c6e299 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -404,7 +404,7 @@ From our collection of SD-files, we first extract all stored values into tabular > > {% snippet faqs/galaxy/tools_select_collection.md datatype="datatypes" %} > -> 3. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 3. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} - interconvert between various chemistry and molecular modeling data files with the following parameters: > - {% icon param-file %} *"Molecular input file"*: choose one of the SD-files from the collection generated by the docking step. > - {% icon param-file %} *"Output format"*: `Protein Data Bank format (pdb)` > - {% icon param-file %} *"Split multi-molecule files into a collection"*: `Yes` From 4d32f08ff3d754ecb32f900e4f6fd49c0df4fbd4 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:47:20 +0530 Subject: [PATCH 18/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index fd0fbd88c6e299..d059c7dda15839 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -366,7 +366,7 @@ Taylor-Butina clustering ({% cite Butina1999 %}) provides a classification of t > 1. {% tool [Taylor-Butina clustering](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/1.5) %} of molecular fingerprints with the following parameters: > - {% icon param-file %} *"Fingerprint dataset"*: 'Fingerprints' file. > - {% icon param-file %} *"threshold"*: `0.8` -> 2. {% tool [NxN clustering] of molecular fingerprints (toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1) %} with the following parameters: +> 2. {% tool [NxN clustering](toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/1.5.1) %} of molecular fingerprints with the following parameters: > - {% icon param-file %} *"Fingerprint dataset"*: 'Fingerprints' file. > - {% icon param-file %} *"threshold"*: `0.0` > - {% icon param-file %} *"Format of the resulting picture"*: `SVG` From 83acb85531865095f243c6b0d70c80d025663eb1 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:47:34 +0530 Subject: [PATCH 19/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index d059c7dda15839..43fb70d2bac069 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -348,7 +348,7 @@ Before clustering, let's label each compound. To do so add a second column to th > - {% icon param-file %} *"File to process"*: `Ligand SMILES`. > - {% icon param-file %} *"Find pattern"*: add the current label of the SMILES here. You can find it by clicking the 'view' button next to the `Ligand SMILES` dataset - it will look something like `/data/dnb02/galaxy_db/files/010/406/dataset_10406067.dat`. > - {% icon param-file %} *"Replace with"*: `ligand` -> 2. {% tool [Concatenate datasets] tail-to-head (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/1.0.0) %} with the following parameters: +> 2. {% tool [Concatenate datasets](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/1.0.0) %} tail-to-head with the following parameters: > - {% icon param-file %} *"Datasets to concatenate"*: Output of the previous step. > - Click on **Insert Dataset** and in the new selection box which appears, select 'Compound library'. > - Run the step and rename the output dataset 'Labelled compound library'. From 47103d69337c01161bead1749874b72aa1e25f87 Mon Sep 17 00:00:00 2001 From: Swathi Nataraj <153908478+Swathi266@users.noreply.github.com> Date: Fri, 4 Apr 2025 19:47:45 +0530 Subject: [PATCH 20/20] Update topics/computational-chemistry/tutorials/cheminformatics/tutorial.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- .../tutorials/cheminformatics/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md index 43fb70d2bac069..6a59ed28186576 100644 --- a/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md +++ b/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md @@ -247,7 +247,7 @@ Further, docking requires the coordinates of a binding site to be defined. Effec > 1. {% tool [Prepare receptor](toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/1.5.7+galaxy0) %} with the following parameters: > - {% icon param-file %} *"Select a PDB file"*: 'Protein' PDB file. > - Rename to 'Prepared receptor' -> 2. {% tool [Compound conversion] - interconvert between various chemistry and molecular modeling data files (toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} with the following parameters: +> 2. {% tool [Compound conversion](toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1) %} - interconvert between various chemistry and molecular modeling data files with the following parameters: > - {% icon param-file %} *"Molecular input file"*: 'Compound library' file. > - {% icon param-file %} *"Output format"*: `MDL MOL format (sdf,mol)` > - {% icon param-file %} *"Generate 3D coordinates"*: `Yes`