Database SMART

Other related coding languages are derived from enhancements of SMILES (XSMILES, SMARTS, SMIRKS, STRAPS, CHUCKLES, CHORTLES, CHARTS [22]). Each of them was designed to represent special molecular structures or to allow particular applications (polymers, mixtures, reactions, or database-handling). 

The JME can also serve as a query input tool for structure databases by allowing creation of complex substructure queries (Figure 2-130), which are automatically translated into SMARTS [22]. With the help of simple HTML-format elements the creation of 3D structure queries is also possible, as were used in the 3D pharmacophore searches in the NCI database system [129]. Creation of reac-... 

Another recent database, still in evolution, is the Linus Pauling File (covering both metals and other inorganics) and, like the Cambridge Crystallographic Database, it has a "smart software part which allows derivative information, such as the statistical distribution of structures between symmetry types, to be obtained. Such uses are described in an article about the file (Villars et al. 1998). The Linus Pauling File incorporates other data besides crystal structures, such as melting temperature, and this feature allows numerous correlations to be displayed. 

Similar residues in the cores of protein structures especially hydrophobic residues at the same positions, are responsible for common folds of homologous proteins. Certain sequence profiles of conserved residue successions have been identified which give rise to a common fold of protein domains. They are organized in the smart database (simple modular architecture research tool) http //smait.embl-heidelberg.de. 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

In the detection of repeats using SMART an algorithm is used that derives similarity thresholds that are dependent on the number of repeats already found in a protein sequence (Andrade et al., 1999b). These thresholds are based on the assumption that suboptimal local alignment scores of a profile/HMM against a random sequence database are well described by an extreme value distribution (EVD). The result of this protocol is that acceptance thresholds for suboptimal alignments are lowered below the optimal scores of nonhomologous sequences. 

Multiple alignments of repeats are constructed in an iterative manner. The initial alignment is based on definitions from determined protein structures or else from the literature. In the initial database search step, a profile constructed from the multiple alignment is compared with a sequence database. Top scoring sequences are considered using complementary approaches such as PSI-BLAST and FASTA to provide the two thresholds minimum E value and minimum number of repeats per protein required. After one or two iterations, the final alignment and the thresholds are stored in the SMART database to allow the detection of repeats in any sequence. 

Newly Identified Domain Homologs from Recent SMART Database Update... 

A variety of domain or motif families occur only as extensions to other domains. The Bruton s tyrosine kinase motif (BTK), for example, is found only at the C terminus of PH domains. Similarly, a C-terminal extension (the S TK X domain) to some subfamilies of serine/threonine kinases (S TK) is not found in isolation. Cases where only the extension, and not the preceding domain, is found are strong evidence that the proteins are wrongly assembled from genomic sequence or else represent partial cDNA sequences (Fig. 9, see Color insert). Indeed, all five proteins annotated in SMART as containing a S TK X domain with no catalytic domain are noted to be fragments in their corresponding sequence database entries. 

Letunic, 1., et al., SMART 4.0 towards genomic data integration. Nucleic Acids Res, 2004, 32 Database issue, D142-4. 

When a novel homology domain has been discovered, it is possible to store the corresponding domain descriptor (profile or HMM) in a number of dedicated domain databases, which can be used to analyze newly identified sequences for their domain content [9, 10]. Several competing domain- and motif-databases exist, including PROSITE, PFAM, SMART, and Superfam, which contain descriptors for most, if not all, of the known domains involved in the ubiquitin system [11-14]. Recently, a new meta-database named INTERPRO has been established, which tries to combine the descriptors of several domain databases under a single user interface [15]. Pointers to the very useful search engines of the domain databases are provided in Table 12.1. 

University of Alberta. Educational Software for Micromachines and Related Technologies. Available online. URL http //www. cs.ualberta.ca/ database/MEMS/sma mems/index2.html. Accessed May 28,2009. Research groups at the University of Alberta in Canada constructed this Web resource, which discusses a variety of smart materials, including shape-memory alloys, piezoelectric materials, and electrorheological and magnetorheological fluids. 

The number of features in the maximal feature vector, of order of hundreds of thousands, is too big to be useful in practice, due to such issues like data transmission through the net, data storage in databases, templates comparison made in smart card processors or biometric standalone devices, etc. To reduce the number of features, we will look for a feature vector that leads to minimum sample equal error rate determined on available iris images database. 

SMA/MEMS Research Group. Smart Materials." Available online. URL http //www.cs.ualberta.ca/ database/MEMS/sma mems/smrt.html. Last modified on August 17, 2001. 

A variety of databases and online tools exist to facilitate searches for protein motifs (Table 6). The most comprehensive resource for the detection of large protein motifs is the Conserved Domain Database (CDD) provided by NCBI. The CDD includes all data present in the SMART and PFAM databases, along with some manually curated entries. All protein-protein BLAST... 

SMART Database and search tools smart.embl-heidelberg.de... 

Abalos E, Duley L, Steyn DW, Henderson-Smart DJ (2007) Antihypertensive drug therapy for mild to moderate hypertension during pregnancy. Cochrane Database of Systematic Reviews Issue 1. Art. No. CD002252. DOI 10.1002/14651858. 

Recently, we started working with our undergraduate Ventures Scholars who were seeking to go into graduate programs. If you are interested in obtaining a database of these students, please call us at 1-800-94-SMART, extension 103. 

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