Classification family

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. 

S Henikoff, JG Hemkoff. Pi otem family classification based on searching a database of blocks. Genomics 19 97-107, 1994. 

Liu, W., Ahlert, J., Gao, Q. et al. (2003) Rapid PCR amplification of minimal enediyne polyketide synthase cassettes leads to a predictive familial classification model. Proceedings of the National Academy of Sciences of the United States of America, 100, 11959. 

Under this framework. Fig. 6 shows the basic pieces for constructing annotated chemical libraries. On the one hand, proteins should be stored using the appropriate annotation under their respective protein-family classification schemes (in this case, nuclear receptors). On the other hand, molecules should be stored using a unique hierarchical identifier. The link between the two entities (molecules and proteins) would be defined by pharmacological data (activity). The use of a certain criteria would then allow to construct a binary annotation matrix, from which the mapping of the chemogenomic space is established. 

Koua D, Cerutti L, Falquet L et al (2009) PeroxiBase a database with new tools for peroxidase family classification. Nucleic Acids Res 37 D261-D266... 

A chemotype describes the subspecies of a plant that have the same morphological characteristics (relating to form and structure) but produce different quantities of chemical components in their essential oils. This again is widespread within the botanical family classification of the Labiatae or Lamiaceae. Examples of plants producing essential oils with different chemotypes include lavender, melissa, peppermint, basil, rosemary, sage and thyme. 

These are arranged in their botanical family classification. Amounts quoted are either % typical ranges or typical analysis amounts. 

Ferran Ferran, 1992 Family Classification 2L/Kohonen Freq/Map(7x7)... 

Figure 11.1 MOTIFIND neural network design for protein family classification.

As a full-scale family classification system, more than 1200 MOTIFIND neural networks were implemented, one for each ProSite protein group. The training set for the neural networks consisted of both positive (ProSite family members) and negative (randomly selected non-members) sequences at a ratio of 1 to 2. ProClass groups non-redundant SwissProt and PIR protein sequence entries into families as defined collectively by PIR superfamilies and ProSite patterns. By joining global and motif similarities in a single classification scheme, ProClass helps to reveal domain and family relationships, and classify multi-domained proteins. 

Coutinho PM, Deleury E, Davies GJ, Henrissat B (2003) An evolving hierarchical family classification for glycosyltransferases. J Mol Biol 328 307-317... 

The ketone functional group appears in a wide variety of natural products ranging from the simple terpenes to complex macrocycles and polyfunctional molecules. This section will focus on simple, naturally-occurring ketones, largely from the terpene family, which illustrate relationships between structure and 1 0 NMR chemical shifts. Other more complex ketone containing structures will be examined later according to their natural product family classification, e.g. chromones, flavones, etc. 

Selection of databases on protein structure and protein family classification ... 

A comprehensive description of the databases and methods for domain, family, and pattern identification is available in chapter 2. Therefore, in this chapter, the discussion of the application of family and domain information to function assignment will be limited to Pfam, the virtual standard in protein domain/family classification, and to InterPro and CDD, two resources that integrate multiple domain databases. In addition, I discuss tools that can be used to scan those databases, namely HMMER,... 

AIkylpiperidine Derivatives as Phylogenetic Characters for a Family Classification... 

Family Fabiatae (Famiaceae) consists of aromatic herbs or shrubs which are widely distributed around the Mediterranean coast and many other parts of the world. There are about 200 genera in Labiatae family. Since the absence of a satisfactory intra-familial classification, the genera are arranged in the following informal sequence in Turkey [7]. 

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