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CASP9

© 2010 Grishin lab/HHMI/UTSW

updated on 2010-12-16

Targets
515	516	517	518
519	520	521	522
523	524	525	526
527	528	529	530
531	532	533	534
535	536	537	538
539	540	541	542
543	544	545	546
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551	552	553	554
555	556	557	558
559	560	561	562
563	564	565	566
567	568	569	570
571	572	573	574
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579	580	581	582
583	584	585	586
587	588	589	590
591	592	593	594
595	596	597	598
599	600	601	602
603	604	605	606
607	608	609	610
611	612	613	614
615	616	617	618
619	620	621	622
623	624	625	626
627	628	629	630
631	632	633	634
635	636	637	638
639	640	641	642
643

Domain definition

Proteins are composed of domains. Domains are usually defined as globular units in protein structures. Domains are somewhat separate from each other spatially and can recombine with each other in evolution to form various proteins. Each domain frequently carries out its own function, or the functional site may be formed at the domain interface. Analysis of domains is essential for understanding of proteins. However, while everyone agrees on the domain importance, opinions differ greatly about the criteria for domain definition, and existing software tools are inconsistent with each other in domain parse. Researchers think about domains from the position of structural compactness, sequence similarity and continuity, evolutionary origin, folding or function. Different criteria lead to different domain definitions. Nevertheless, our experience with protein sequence-structural analysis indicates that it might be possible to bring these criteria together for a biologically reasonable domain parse. We applied our conceptual view on protein domains to CASP9 targets. Domains defined here correspond to structurally compact evolutionary modules.

To define domains in a target we looked for similarity to other protein sequences and structures and self-similarity (internal duplications), structural compactness (globularity), presence of a hydrophobic core, and took into account sequence continuity. To define precise boundaries between domains, we inspected side-chain orientations and their interactions with domains. In some targets (e.g. T0530), certain regions protruded away from the PDB chain. These regions were frequently involved in a domain swap. In such cases, we defined globular domains with a swap. The following targets were affected by this:

• T0530_1s, T0536_1s, T0600_1s and T0637_1s, are domains with a Swap
• T0521_1s is a domain with a swap of chain B with a symmetry mate D (asymmetric unit does not contain chain D, this chain was generated by crystallographic symmetry)

In other cases, protruding regions did not participate in swaps, but were interacting with other chains in the crystals, e.g. in T0516. We removed such regions in domain definition to check whether the shorter domain is predicted more accurately. Text file with domain boundaries for all targets can be downloaded from here.

We did not take into account server predictions in defining domains, only sequence, structural and evolutionary considerations about targets were used. It might not be necessary to use these evolutionary domains for evaluation of all targets. See the discussion of whole chain vs. domain evaluation. In summary, comparison of domain-based predictions with whole chain predictions reveals that the following targets require domain-based evaluation: T0521, T0528, T0529, T0533, T0534, T0542, T0543, T0544, T0547, T0548, T0550, T0553, T0555, T0571, T0575, T0579, T0582, T0586, T0589, T0596, T0600, T0604, T0608, T0611, T0628, T0629, T0632, as for these targets server predictions for whole chains are much inferior to individual domain predictions. Only these targets are evaluated as domains in our combined domain evaluation tables. Furthermore, among those domains, we merged T0533_1 and T0533_3 as one evaluation unit, similar cases are T0542_2 and T0542_3, T0543_3 and T0543_4, T0589_1 and T0589_2. Predictions for other targets follow the general trend, are of a more similar quality for 'domain' and 'whole chain' and thus domain-based evaluation may not be necessary for them. Thus other targets are evaluated as whole chains in combined domain evaluation tables. These targets are considered to be single-domain proteins for evaluation. Although some of these targets are multi-domain proteins evolutionarily, domains do not move relatively to each other, are of the same prediction difficulty. Nevertheless, we compute evaluation scores on all domains shown in the table below, and these scores are available from individual target pages,e.g. T0515 page shows evaluation of whole chain (T0515), which is the evaluation unit we finally used, N-terminal Tim-barrel domain (T0515_1) and C-terminal Eukaryotic ODC-like domain (T0515_2).

In the table below, domains are marked by "_" followed by a domain number and preceded by a target name; "s" after the domain number denotes a swapped domain. Whole chains (no "_" in name) are given to show the residue range and mapping between target and PDB. Links to PyMOL scripts with domain definitions by various workers and programs are provided as well.