Prince:Notebook/PPIX/Determine All Crosslink Possibilities

Determine all the PDB files with 2 or more proteins
It is unclear to me the best/proper way to get at all the protein interactions found in PDB [JTP]

The Advanced Search options, selecting assymetric units with 2-100000 chains provides 16441 files for download (≈11 GB). *Ryan M Taylor 14:07, 13 May 2010 (EDT): List of Complexes

Applied method

 * 1. Determine all novel crosslinks existant between primary nitrogens of Lys residues under 200 Angstroms in length.
 * 2. Tunnel through the crosslink vector, determining if there are any atoms within about 3.5 Angstroms from every point of the vector
 * : i. This provides % outsideness, allowing for estimation of feasibility of the cross link.
 * 3. Export to .yml file, providing a database for further testing.
 * 4. Created pymol interaction script to generate images showing the crosslinks mapped to the PDB.

 Available via GitHub
 * github code repository

Uncoded Alternatives

 * Could do some kind of fill algorithm
 * specify points that are outside, subdivide into grid and walk and mark


 * Odd / even intersection
 * link to discussion


 * Precalculating plane equations
 * link


 * Does a ray intersect a triangle? (if you don't have plane equations)
 * link

Is a residue even solvent accessible?
SABLE [Solvent AccessiBiLitiEs of amino acid residues ]