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Searching for Flavin Interactions with the Protein Data Bank:

Searching for Generic Flavin Information:

1. Choose a PDB file
2. Selects key HETRATMS

• select HTRATOMS from the PDB

3. Return information based on:
   1. Cartesian Distance between ATMS/HTRATMS
   2. Vector Angles between relevant ATMS/HTRATMS (Return information for the moment to be stored as a text file)

REQUIREMENTS:

1. Necessary storage format definition
2. Filter interactions between atoms that fit criteria for distance AND angle
3. Need a small sample of testable data
4. Classify Chemical type

SOLUTIONS TO REQUIREMENTS:

1. Filter Interactions by distance using Van der Waal’s distances NOTE: should be able to be flexible i.e. could input your own distance and check
2. Use PyMol to visualize and check results
3. Using biopandas code already developed to parse through pdb files link to biopanda documentation/files: https://github.com/rasbt/biopandas

Searching for different Interaction Clusters:

1. User inputs key interactions
2. Generate list of Clusters based on interaction input
3. Output the information as a text file

REQUIREMENTS:

1. Define what we store for clusters
2. Determine size of feature space
3. Define scoring algorithm to to find similarity with clusters
4. Small test data set
5. Determine cluster model and tune model

Current Flavin codes being searched for in PDB files:

•	FMN
•	FAD
•	6FA

Storage Formats being used:

MongoDB • link: mongodb://umich:[email protected]:63124/flavoinformatics GitHub • link: https://github.com/antoniomika/FlavinDB