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The IsoMIF Finder Interface allows you to identify binding site molecular interaction field (MIF) similarities between a query protein structure and a database of pre-calculated MIFs or user defined cavity MIFs. For detailed information on IsoMIF please see the paper below:

Chartier M. and Najmanovich R. (2015) Detection of Binding Site Molecular Interaction Field Similarities. Journal of Chemical Information and Modeling. PubMed | JCIM | PDF

Chartier M., Étienne Adriansen and Najmanovich R. (2015) IsoMIF Finder: online detection of binding site molecular interaction field similarities. Bioinformatics, Oxford Journals. PubMed | Bioinformatics | PDF

See results example page.
Git Page

Download Pre-Calculated Mifs

Got a question?

1. Select a query PDB

PDB: 4-letter PDB code

Upload one

2. Define cavity on query PDB

Molecular interaction fields are calculated in the volume of cavities of the query PDB. You will be able to crop the cavities found.

Find top cavities (Max. 5) Identified in a purely geometric manner


Crop around a ligand :
3-letter ligand name in the PDB file
Ligand number (up to 4 characters)
Alternate location (optional)
Crop cavity at this distance around the ligand (in Å)

3. Compare query MIF to

Precalculated MIF(s):

My PDB list Cavities will be identified in each PDB structure.

One per line, in one of the 3 following formats:

Finds the largest cavity of PDB 1LHU.

1LHU 3
Finds the top 3 largest cavities.

1LHU EST 301 A
Find the cavity in contact with ligand EST 301 A
User must provide the ligand PDB name, Number, Chain and optionally the alternate location.

4. Parameters

Grid spacing:
Geometric Distance Threshold:
The number of top results: (max. 250) Full list of hits will be downloadable in CSV format.
Generate PyMol sessions to visualize the top hits (max. 100).

5. Email notifications (optional)

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