Contents - annotations

LSKB Database provides following chemical annotations

• Compound names, CAS ID, ZINC compounds, PubChem ID, FDA-approved drugs, DrugBank basic information
• Names registered in PubChem Substance
• Names and keywords registered in MeSH
• Information on target genes tested in bioassays
• PDB complex compounds
• Compound names registered in DrugBank as well as relevant detail information about target genes for treatments, development code, and target proteins
• Information on relevant literature entries
• The rankings of genes related Chemicals, or disease related chemicals that is listed in the literature

Using these annotations, the following types of searches can be conducted:

• Search for compounds containing drugs demonstrating activity in a similar type of assay.
• Search for compounds with the same target protein.
• Search for compounds with the same pharmacological action
• Search for target proteins using literatures, bioassays, or PDB ligands
• Analyzing of the ontology of proteins in compound clusters
• Search for active compounds of each protein using a bioassay as data source
• Search for binding ligands using PDB data as data source
• Register and uniformly manage in-house compounds in LSKB.
• The followings are examples of using the above mentioned features:

Key function with structure

The system allows to perform both chemical structure and keyword searches.
The structure searches takes structures copied to an SD file or the Clipboard and performs similarity or exact match searches against “Chemicals in literatures”, “all PubChem”, “DrugBank”, “FDA”, “ZINC”, “PDB complex compounds”, and “datasets defined in LSKB synonym dictionaries”.

• Searches based on Exact Match、Similarity search (UNITY Fingerprint), and Substructure search
• Parameters for search filters - Rule of Five, molecular weight, and mlogP - can be specified by the Donor/Acceptor
• Perform batch searches by multiple compound structures.
• All compounds or selected compounds from SDF or Smiles files can be searched simultaneously
• Conduct similarity calculations between selected compounds and compounds included in other spreadsheets
• Export data to a text file
• Use a compound list to search for related proteins in the LSKB