Domain classification

Chain dynamics regional domain classification chain conformation (gauche vs. Irons)... 

Roberts DW, Patlewicz G, Kern PS et al (2007) Mechanistic applicability domain classification of a local lymph node assay dataset for skin sensitization. Chem Res Toxicol 20(7) 1019-1030... 

Action patterns Adhesion domains Affinity and mechanism-based inhibitors Catalytic domains Classification schemes Hydrolases Lyases Mechanism of action Phosphorylases Proteinaceous inhibitors... 

Tomme P, Warren AJ, Miller Jr. RC, KUburn DG, GUkes NR (1995) Cellulose-binding domains classification and properties. In Saddler JN, Penner MH (eds) Enzymatic degradation of insoluble carbohydrates. American Chemical Society, Washington, DC, pl42 Irwin D, Walker L, Spezio M, Wilson D (1993) Biotech Bioengin 42 1002... 

Some biologists prefer a three-domain classification scheme— Bacteria (eubacteria), Archaea (archaebacteria), and Eukarya (eukaryotes)—to the five-kingdom classification (Figure 1.19). The basis for this preference is the emphasis on biochemistry as the basis for classification. 

In the three-domain classification schemes, eukaryotes have a domain to themselves. Two domains consist of prokaryotes. Eubacteria are the commonly encountered prokaryotes. Archaea are organisms that live in extreme environments such as those that were found on the early Earth. 

ADDA http //ekhidna.biocenter.helsinki.fi 8080/examples/ servlets/adda/ Prot domain classif and singleton... 

Topology, and Homologous (CATH) superfamilies classification and the domain classification based on the Distance ALIgnment (DALI) algorithm. Finally, the tutorial concludes with a discussion of the future of protein structure classifications. 

This two-stage method, implemented in DALI, has been used to compare representatives from all nonhomologous (in sequence) families in the protein data bank. " More details are given in the DALI Domain Classification below. 

The DDD, also called the DALI domain classification, is derived from a... 

Groos JC, Ritter JRR (2009) Time domain classification and quantification of seismic noise in an urban environment. Geophys J Int 179 1213-1231... 

Much surface work is concerned with the local atomic structure associated with a single domain. Some surfaces are essentially bulk-temiinated, i.e. the atomic positions are basically unchanged from those of the bulk as if the atomic bonds in the crystal were simply cut. More coimnon, however, are deviations from the bulk atomic structure. These structural adjustments can be classified as either relaxations or reconstructions. To illustrate the various classifications of surface structures, figure A1.7.3(a ) shows a side-view of a bulk-temiinated surface, figure A1.7.3(b) shows an oscillatory relaxation and figure A1.7.3(c) shows a reconstructed surface. 

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH—A hierarchic classification of protein domain structures. Stnrcture 5 1093-1108, 1997. 

In Figure 2.6, the slips/mistakes distinction is further elaborated by relating it to the Rasmussen SRK classification of performance discussed earlier. Slips can be described as being due to misapplied competence because they are examples of the highly skilled, well practiced activities that are characteristic of the skill-based mode. Mistakes, on the other hand, are largely confined to the rule and knowledge-based domains. 

Error probabilities that are used in decomposition approaches are all derived in basically the same manner. Some explicit or implicit form of task classification is used to derive categories of tasks in the domain addressed by the technique. For example, typical THERP categories are selections of switches from control panels, walk-around inspections, responding to alarms and operating valves. 

There are two major data-type classifications time-domain and frequency-domain. Each of these can be further divided into steady state and dynamic data formats. In turn, each of these two formats can be further divided into single-channel and multi-channel. 

In order to make as much data on the structure and its determination available in the databases, approaches for automated data harvesting are being developed. Structure classification schemes, as implemented for example in the SCOP, CATH, andFSSP databases, elucidate the relationship between protein folds and function and shed light on the evolution of protein domains. 

Cadherins are a superfamily of Ca2+-sensitive cell-cell adhesion molecules, which cause homophilic cell interactions. Cadherins can be divided into different subfamilies, namely, classical cadherins, desmosomal cadherins, protocadherins, and nonconventional cadherins (7TM cadherins, T-cadherin, FAT). Classical cadherins are often denoted by a prefix reflecting their principal expression domains e.g., E is epithelial, N is neuronal, and P is placental. However, this classification is not stringent, as for instance E-cadherin can also be found in certain neuronal tissues, and N-cadherin is also found in epithelial cells. Among the desmosomal cadherins, two subfamilies can be distinguished the desmocollins 1-3 and the desmogleins 1-4. 

Peptidases have been classified by the MEROPS system since 1993 [2], which has been available viatheMEROPS database since 1996 [3]. The classification is based on sequence and structural similarities. Because peptidases are often multidomain proteins, only the domain directly involved in catalysis, and which beais the active site residues, is used in comparisons. This domain is known as the peptidase unit. Peptidases with statistically significant peptidase unit sequence similarities are included in the same family. To date 186 families of peptidase have been detected. Examples from 86 of these families are known in humans. A family is named from a letter representing the catalytic type ( A for aspartic, G for glutamic, M for metallo, C for cysteine, S for serine and T for threonine) plus a number. Examples of family names are shown in Table 1. There are 53 families of metallopeptidases (24 in human), 14 of aspartic peptidases (three of which are found in human), 62 of cysteine peptidases (19 in human), 42 of serine peptidases (17 in human), four of threonine peptidases (three in human), one of ghitamicpeptidases and nine families for which the catalytic type is unknown (one in human). It should be noted that within a family not all of the members will be peptidases. Usually non-peptidase homologues are a minority and can be easily detected because not all of the active site residues are conserved. 

The Dirichlet difference problem in a domain of rather compHcated configuration. If a solution of the Dirichlet problem needs to be determined in a domain G with a nonlinear boundary, the grid ( f G) is, generally speaking, non-equidistant near the boundary. We describe below such a grid and give the possible classification of its nodes. 

We offer below more a detailed classification of inner nodes. With this aim, let us draw up a straight line parallel to the axis Ox through an inner node X Its intersection with the domain G is an interval (or several... 

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