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PSW-Designer_​v1.0_​Linux

Ligand Miner Photoswitchable Library Builder Screeening & Scoring Node check: For a sucessfull execution, all the nodes displayed below need to be avaible. Please, refer to the installationinstructions in case some node is missing. ## INSTALLATION INSTRUCTIONSTo run this workflow you need to have KNIME v4.7.5 or above and a local copy of the ChEMBL database (v33, http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_33_sqlite.tar.gz).1) Activate the following update sites in Knime Preferences > Install/Update > Available Software Sites KNIME Update site: https://update.knime.com/analytics-platform/4.7 KNIME Community experimental: https://update.knime.com/community-contributions/4.7 KNIME Community trusted: https://update.knime.com/community-contributions/trusted/4.7 KNIME Partner Update: https://update.knime.com/partner/4.72) Add these new update sites in nime Preferences > Install/Update > Available Software Sites > Add NodePit: https://download.nodepit.com/4.7 Palladian KNIME nodes: https://download.nodepit.com/palladian/4.7 BioSolveIT: https://www.biosolveit.de/KNIME/download/biosolveit_knime_nodesWith this, it should automatically find all the missing nodes needed to execute the workflow when it is open for the first time. 3) Create a Conda environment called ‘psw’ with specific libraries by running the following commands in your Unix-based terminal (assuming Conda is installed): #Create conda environment $ conda create -n psw python=3.9 # Active the enviroment $ source activate psw # Install dependencies and necessary packages $ conda install -c conda-forge rdkit py4j pyarrow openmm numpy scipy mpi4py openbabel $ pip install --upgrade propka pdb2pqr## Please, cite us: ## TroubleshootingLINUX: In case of a problem executing the Protein Preparation component (error in PDBFixer python component, `GLIBCXX_3.4.30' not found), do: $ conda install -c conda-forge libstdcxx-ng=12 ChEMBL Miner Data Filtering Ligands & Reactions Descriptors Prediction Protein Selection Reactor Protein Preparation Docking Data Processing PhotoswitchableFilter Ligand Preparation Regex Extractor Ligands andProteins Viewer PDB Loader Molecule Converter(Naomi) MarvinSketch Mol2 Writer RDKit From Molecule OpenBabel Ligand Miner Photoswitchable Library Builder Screeening & Scoring Node check: For a sucessfull execution, all the nodes displayed below need to be avaible. Please, refer to the installationinstructions in case some node is missing. ## INSTALLATION INSTRUCTIONSTo run this workflow you need to have KNIME v4.7.5 or above and a local copy of the ChEMBL database (v33, http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_33_sqlite.tar.gz).1) Activate the following update sites in Knime Preferences > Install/Update > Available Software Sites KNIME Update site: https://update.knime.com/analytics-platform/4.7 KNIME Community experimental: https://update.knime.com/community-contributions/4.7 KNIME Community trusted: https://update.knime.com/community-contributions/trusted/4.7 KNIME Partner Update: https://update.knime.com/partner/4.72) Add these new update sites in nime Preferences > Install/Update > Available Software Sites > Add NodePit: https://download.nodepit.com/4.7 Palladian KNIME nodes: https://download.nodepit.com/palladian/4.7 BioSolveIT: https://www.biosolveit.de/KNIME/download/biosolveit_knime_nodesWith this, it should automatically find all the missing nodes needed to execute the workflow when it is open for the first time. 3) Create a Conda environment called ‘psw’ with specific libraries by running the following commands in your Unix-based terminal (assuming Conda is installed): #Create conda environment $ conda create -n psw python=3.9 # Active the enviroment $ source activate psw # Install dependencies and necessary packages $ conda install -c conda-forge rdkit py4j pyarrow openmm numpy scipy mpi4py openbabel $ pip install --upgrade propka pdb2pqr## Please, cite us: ## TroubleshootingLINUX: In case of a problem executing the Protein Preparation component (error in PDBFixer python component, `GLIBCXX_3.4.30' not found), do: $ conda install -c conda-forge libstdcxx-ng=12 ChEMBL Miner Data Filtering Ligands & Reactions Descriptors Prediction Protein Selection Reactor Protein Preparation Docking Data Processing PhotoswitchableFilter Ligand Preparation Regex Extractor Ligands andProteins Viewer PDB Loader Molecule Converter(Naomi) MarvinSketch Mol2 Writer RDKit From Molecule OpenBabel

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: icaro
Created at: 2023-01-13
On NodePit since: 2023-09-20
Last update: 2024-04-27
Created with KNIME version: v4.7.5

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