Domain assignments

Vibrational domain Assignment Ceh factor group symmetry Raman (cm ) IR (cm )... 

By combining these thresholds, we generate datasets of various qualities (Levels A, B, C, and D. see http //sevens.cbrc. jp/for details). The most accurate dataset (Level A, reeNote 4) is obtained by AND combination of the threshold of sequence similarity search (E value <10" °) and PFAM domain assignments (E value < 10 °), and has 99.4% sensitivity and 96.6% specificity for known GPCR datasets. 

If a reflected point should be outside the possible experimental domain, assign a very poor result to this vertex, e.g. the yield = 0%. 

Fig. 48. AFM phase image of pSt-b-pBzA hybrid nanoparticle (sub) monolayer on mica. Domain assignments dark spots (polysilsesquioxane particles), dark corona around particles (tethered pSt, Mn=5,250 Mw/Mn=1.22) light continuous matrix (tethered pSt-b-pBzA), Mn= 27,280 Mw/Mn=1.48). Reprinted with permission from [338]. Copyright (2001) American Chemical Society.

Domain assignment domains are basic building blocks of protein 3D structures. Several algorithms have been proposed to identify domains in a protein structure using criteria such as physico-chemical properties of amino acids in certain regions, e.g. hydrophobicity and accessibility, compactness of protein parts and their recurrence in other proteins [116-120]. 

Jones, S., et al., Domain assignment for protein structures using a consensus approach characterization and analysis. Protein Sci, 1998. 7(2) p. 233-42. 

Direct Domain Assignment through Search in Domain/Family Databases... 

Marsden, R. L., L. J. McGuffin, and D. T. Jones. 2002. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci 11 2814-24. 

Domain Assignment through Indirect Evidence Domain Predictors... 

Fig. 3. STM images of the passive film formed on Cr(l 10) in 0.5M H2SO4 at +500 mV/RHE. The left image shows the disordered protrusions of nanoscopic dimensions. The right images show a small ordered domain assigned to a nanocrystal of oxide (a-Cr203(0001)) at two different magnifications.

Domain assignment (i.e. protein structure similarity clustering)... 

Table 3 Websites for Publicly Available Services or Programs for Protein Domain Assignment ...

SCOP, CATH, and DDD agree on most of their classifications, despite differences in the classification methods they have implemented, and in the rules of protein structure and taxonomy they are based on. Hadley and Jones were the first to publish a detailed comparison of the fold classifications produced by SCOP, CATH, and FSSP. They showed that the three classification systems tend to agree in most cases, and that the discrepancies and inconsistencies are accounted for by a small number of problems. Among these, the domain assignment plays a crucial role. As mentioned, the separation of proteins into domains is a difficult and often subjective process. Many... 

Domain Assignment for Protein Structures Using a Consensus Approach Characterization and Analysis. 

Database which contains descriptive information about knowledge in a database, including domain assignment, ownership, access restrictions, database model. Other definitions are given in the text. 

Figure 5. Final domain assignments of nine-membered enediyne PKSEs from C-1027producer S. globisporus and the NCSproducer S. carzinostaticus. Active site serines within ACP domains arephosphopantetheinylated by PPTdomain (in cis) followed by production of the polyene precursor to the enediyne core. R, 3, 5 -adenosine diphosphate.

---