PSW-Designer

INSTALLATION INSTRUCTIONS To 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/4.7 2) 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_nodes With 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 ## Troubleshooting LINUX: 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 ## Please, cite us: (1) Simon, I. A.; Homan, E. J.; Wijtmans, M.; Sundström, M.; Leurs, R.; De Esch, I. J. P.; Zarzycka, B. A. PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands. J. Chem. Inf. Model. 2023. https://doi.org/10.1021/acs.jcim.3c01050. © 2023 Icaro A. Simon Division of Medicinal Chemistry Vrije University Amsterdam All rights reserved.

Last edited  Mar 8, 2023 11:04 AM

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Last edited  Jun 15, 2022 8:58 AM