MMsINC Ligand & Structure PDB Search allows users to query the databse compounds using Ligand PDB.
You can draw a Ligand PDB chemical structure using JME
or passing as input directly the SMILES or PDB codes. In fact the browser allows you to give a list of PDB codes. The list can contain up to 5 PDB codes.
All the MMsINC Ligand & Structure PDB Search are similarity searches using the Tanimoto coefficient to determine the similarity.
This query of similarity is identical to the similarity search for the MMsINC Structure Search.
SMILES: The "simplified molecular input line entry specification" or SMILES is a specification to describe unambiguously the structure of chemical molecules using short ASCII strings.
PDB:Protein Data Bank accession number. You can insert a list of PDB codes delimited by a comma (example: 100D , 101D , ...). The list is limited to 5 PDB codes.
Similarity search retieves similar compounds to the chemical structure given in input, using the tanimoto co-efficient. The similarity is measured using the Tanimoto equation and a binary fingerprint, called molecular fingerprint, computed for every structure. A molecular fingerprint is a bit sequence where
each bit in the fingerprint (or fragment bit-string) represents one molecular fragment.
Molecular fingerprint. The yellow represents the presence of the fragment in the molecule whereas the blue the abscence.
The bit string for a molecule records the presence (1) or absence (0) of each fragment in the molecule. The fingerprint-based similarity is the comparison between two fingerprints to find the common bits, and then compute the Tanimoto coefficient.
The number of similar compounds extracted depends on the threshold value of the tanimoto co-efficient. The values available for the tanimoto are 0.85, 0.90 and 0.95.
You can search by similarity only if your input is a SMILES
In order to be able to search Ligand PDB using MMsINC, you must click on the "MMsINC Search" button because the "Structure Search" is selected by default, as described in the figure below.
This Search mode present two types of query that we will describe in the two following scenarios.
I) Scenario 1: Search All the Ligand PDB which are similar to a structure depicted or SMILES given as input.
1. Enter the SMILES string in the textfield called "Query Data", or you can generate you SMILES from the structure depicted, using the JME applet.
2. Select the Tanimoto coefficient value that you want to use for your search.
3. Click on the "Search" in order to retrieve the Ligand PDB which are similar to your input.
MMsINC presents to the user the identified PDB ligands retrieved from the request submited in the figure above, with their structural diagram and the ligand code.
Selecting a specific ligand takes the user to the ligand report page
II) Scenario 2: Search All the Ligand PDB from a list of PDB codes given as input.
1. Enter a list of up to five PDB codes, in the textfield called "Query Data".
2. Click on the "Search" in order to retrieve the Ligand PDB present in this List.
It is possible that some PDB existing codes are not presents in MMSINC because we decided to keep only the proteins whose their ligands have a Tanimoto index superior at least 0.7 to our molecules.
MMsINC displays to the user the identified PDB ligands retrieved from the request submited in the figure above, with their structural diagram and the ligand code.
Selecting a specific ligand takes the user to the ligand report page
