PDB: Binary Complexes

[Marco Gallotta]

Hey all

I need to collect a large set of protein structures from the PDB
containing two or more protein complexes. I will be using this to
extract the information of the protein binding sites, hence the
requirement that they contain two or more complexes.

Anyone familiar with the PDB know of a way to search for structures
meeting this criteria? I've been trying the advanced search, but
cannot seem to find the required search terms. If I can't automate the
search I'll have to do this manually by extracting PDB id's from
papers, which is not fun!

Marco

--
Marco Gallotta
MSc Student | SACO Scientific Committee | ACM ICPC Coach
Department of Computer Science, University of Cape Town
people.cs.uct.ac.za/~mgallott | marco-za.blogspot.com
marco AT gallotta DOT co DOT za | 073 170 4444 | 021 552 2731

[lucky]

R u looking for a specific protein structure or all know protein
structure...like pfam database

[Marco Gallotta]

Right now I'm looking for all protein structures, so the only filter
I'm interested in is "does this structure include more than one
protein complex?".

Later on I will categorise the collection to see if my method works
better when protein family is taken into account.

Marco

[Marco Gallotta]

Got a script to mirror the entire PDB, which should allow me to run a
full analysis and get me the results I need. So my questions has been
answered for now.

Marco