DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile

Abstract

Dividing protein structures into domains is proven useful for more accurate structural and functional characterization of proteins. Here, we develop a method, called DDOMAIN, that divides structure into DOMAINs using a normalized contact-based domain-domain interaction profile. Results of DDOMAIN are compared to AUTHORS annotations (domain definitions are given by the authors who solved protein structures), as well as to popular SCOP and CATH annotations by human experts and automatic programs. DDOMAIN's automatic annotations are most consistent with the AUTHORS annotations (90% agreement in number of domains and 88% agreement in both number of domains and at least 85% overlap in domain assignment of residues) if its three adjustable parameters are trained by the AUTHORS annotations. By comparison, the agreement is 83% (81% with at least 85% overlap criterion) between SCOP-trained DDOMAIN and SCOP annotations and 77% (73%) between CATH-trained DDOMAIN and CATH annotations. The agreement between DDOMAIN and AUTHORS annotations goes beyond single-domain proteins (97%, 82%, and 56% for single-, two-, and three-domain proteins, respectively). For an "easy" data set of proteins whose CATH and SCOP annotations agree with each other in number of domains, the agreement is 90% (89%) between "easy-set"-trained DDOMAIN and CATH/SCOP annotations. The consistency between SCOP-trained DDOMAIN and SCOP annotations is superior to two other recently developed, SCOP-trained, automatic methods PDP (protein domain parser), and DomainParser 2. We also tested a simple consensus method made of PDP, DomainParser 2, and DDOMAIN and a different version of DDOMAIN based on a more sophisticated statistical energy function. The DDOMAIN server and its executable are available in the services section on http://sparks.informatics.iupui.edu.

Figure 1.

The contact-based interaction profile of chain A of protein 1gg3 is shown along with the domains identified by DDOMAIN (solid line), SCOP (dashed line), and CATH (dash dotted line). The residue index here is different from the actual residue number in the PDB structure file because only residues with coordinates are numbered.

Figure 2.

The success rates for the SCOP set as a function of one of the three parameters (E^low_cutoff, E^excess_cutoff, and L_cut) in DDOMAIN with two other parameters fixed. For E^excess_cutoff (dashed curve in the top figure), E^low_cutoff and L_cut are fixed at 0.53 and 34, respectively. For E^low_cutoff (solid curve in the top figure), E^excess_cutoff and L_cut are fixed at 0.36 and 34, respectively. For L_cut (solid curve at the bottom figure), E^low_cutoff and E^excess_cutoff are fixed at 0.53 and 0.36, respectively. This figure explores the variation of the parameters around the optimized values (0.53, 0.36, and 34 for E^low_cutoff, E^excess_cutoff, and L_cut, respectively).