
Here are binary physical interactions for two crystal structures (no
directionality is intended).  

Arp2/3 complex:

Arc18 Arp3
Arp3  Arp2
Arp3  Arc35
Arp2  Arc40
Arc35 Arc40
Arc35 Arc19
Arc19 Arc40
Arc19 Arc15
Arc15 Arc40

Cleavage Factor IA (CFIA) complex:

Clp1	Pcf11
Pcf11	Rna15
Pcf11	Rna14


Notes:

The crystal structure of Arp2/3 was discussed by Bader and Hogue (2003) when
they described their MCODE algorithm.  I think MCODE is probably the closest
competitor of apComplex in terms of complex membership estimation, but the
code is no longer available -- or at least I can't find it.

We discussed the crystal structure and provided a picture of CFIA in our
Biofinformatics paper, so this should probably be referenced and rendered
differently for this paper.


References: 

Bader GD and Hogue CWV.  An automated method for finding molecular complexes
in large protein interaction networks.  BMC Bioinformatics 2003, 4:2.

Robinson RC, Turbedsky K, Kaiser DA, Marchand JB, Higgs HN, Choe S, et al.
Crystal structure of Arp2/3 complex.  Science 2001, 294:1679-1684.

Gross S and Moore C.  Five subunits are required for reconstitutions of the
cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage
factor I.  PNAS USA 2001, 98: 6080-6085.

