Workflows

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

download (2)

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Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

PubChem substructure search (2)

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Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

smiles-identity-idlist (2)

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Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

smiles-identity-idlist (1)

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Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

file-similarity-entrez-url (2)

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Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li