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[ Search PDB | Pocketome | ChEMBL | SureChEMBL | BLAST | UniProt | Ligand Code | Drug Bank | Search PubChem | Historeceptomics ]
The Search tab allows you to search and download content from the following databases:
[ Chemical Substructure | Query Sequence | PDB Field | Load NMR | Occupancy Display | Header | PubMed ]
How to Search the Protein Databank and DownloadThe PDB search tab provides easy access to the PDB database. You can use keyword searching or type in the PDB code you are interested in. An asterisk (*) wildcard can be used to list all the pdb files currently available in the protein databank. Different fields can be searched by using the drop down arrow as shown below. More advanced PDB search tools and how to use the PDB search result table are described in the section entitled Searching the PDB.Once a search is complete a table of PDB files relating to your search query will be displayed. To view the PDB file in 3D in the graphical display double click on a row in the PDBSearchResults table.
There are a number of ways to search the PDB by sequences.
To query the PDB by field (Author, Compound, PDB Header, Experiment Type, Resolution or Ligand Code
Use the PDB Search tab to load NMR structures from the PDB. You can use the drop down button shown below to determine how you want to display your NMR structure. You can choose to display and download the first NMR model, all models in the PDB file or all models in the PDB in a stack. If you choose the stack option the the stack will be stored in the object as described here.
You can use the options in the PDB Search tab to control if and how the partial or zero atom occupancies are displayed. You can choose to circle or label the poor occupancy atoms.
>>load-pdb-hyperlinks{pdb search hyperlinks} h4-- Hyperlinks to PDB Website and UniProt {Hyperlinks to Databases} In the PDB Search Results Table you will see blue hyperlinks that will take you directly to the PDB website or Uniprot website.
To display the PDB Header for a PDB file.
When you search for a PDB file and load it into ICM you will see an icon (shown below) next to your protein name in the ICM Workspace. Click the icon and you will be taken directly to the PubMed primary reference relating to the structure.
The Pocketome (www.pocketome.org) is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank.
ChEMBL (https://www.ebi.ac.uk/chembl/) is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK. To search and download data from ChEMBL:
A table will be displayed as shown below.
The table contains the original activity data without merging or aggregation.
For instance,
Click on the button Get Best Activity to display the best activity for each chemical, protein pair.
For instance,
Chemical 1, Protein 1, Best(Activity 1, 2, 3, ...)
Click on the button Get Ligand Summary to display a list of chemicals with all activities found in ChEMBL.
For instance,
Protein 1, Activity 2
Chemical 2 Protein 1, Activity 1
SureChEMBL (https://www.surechembl.org/search/) provides free access to chemical data extracted from the patent literature. To search SureChEMBL:
To BLAST search the NCBI sequence database:
To find structures containing a particular ligand in the PDB.
To search Drug Bank ( http://www.drugbank.ca/)
The table contains the original activity data without merging or aggregation.
For instance,
Click on the button Get Ligand Summary to display a list of chemicals with all activities found in Drug Bank. The button is located in the extra panel (click on hammer - top right of table panel).
For instance,
Protein 1, Activity 2
Chemical 2 Protein 1, Activity 1
To search PubChem (https://pubchem.ncbi.nlm.nih.gov/):
The historeceptomics (HR) platform is developed by GeneCentrix and reports tissue specific profiling for a drug molecule. It is a unique bioinformatics platform designed to identify mechanism of activity and predict unforeseen effects a chemical might have in the target tissue and off-target tissues. HR integrates data from a variety of sources including:
After searching a results panel as shown below will be displayed. The table is ranked by hr Score and reports the binding affinity gene name and tissue. The p-value represents the chance that the overabundance of the tissue/target in question could occur by random chance based on the variability of the expression of that target across 70 other tissues. Additional plots of gene frequency and hr score for each tissue are reported.
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