The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different "superfamilies", and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor.
The SCOP database is freely accessible on the internet. SCOP was created in 1994. It is maintained by Alexei G. Murzin and his colleagues at the Laboratory of Molecular Biology in Cambridge, England. As of September 2012[update], the current version of SCOP is 1.75 (released June 2009). A snapshot of the next release of SCOP, which is called pre-SCOP (for preview), is accessible from the main SCOP page.
The source of protein structures is the Protein Data Bank. The unit of classification of structure in SCOP is the protein domain. What the SCOP authors mean by "domain" is suggested by their statement that small proteins and most medium sized ones have just one domain, and by the observation that human hemoglobin, which has an α2β2 structure, is assigned two SCOP domains, one for the α and one for the β subunit.
The shapes of domains are called "folds" in SCOP. Domains belonging to the same fold have the same major secondary structures in the same arrangement with the same topological connections. 1195 folds are given in SCOP version 1.75. Short descriptions of each fold are given. For example, the "Globin-like" fold is described as core: 6 helices; folded leaf, partly opened. The fold to which a domain belongs is determined by inspection, rather than by software.
The levels of SCOP are as follows.
The folds are grouped into "classes". The classes are the top level, or "root" of the SCOP hierarchical classification. The classes are displayed something like this:
The number in brackets, called a "sunid", is a SCOP unique integer identifier for each node in the SCOP hierarchy. The number in parentheses indicates how many elements are in each category. For example, there are 284 folds in the "All alpha proteins" class. Each member of the hierarchy is a link to the next level of the hierarchy.
The first few folds of the 284 folds in the "All-α proteins" class are displayed something like the following.
Each fold is followed by a description of that fold.
The domains within a fold are further classified into superfamilies, which, in turn, are classified into families. Within a fold, domains belonging to the same superfamily are assumed to have a common ancestor. However, this ancestor is presumed to be distant, because the different members of a superfamily have low sequence identities. The two superfamilies of the "Globin-like" fold are displayed something like the following:
No description is given for the "Globin-like" superfamily, presumably because its description is very like that of its fold, which has the same name.
Families are more closely related than superfamilies. Domains within a fold are placed in the same family if
The similarity in sequence and structure is evidence that these proteins have a closer evolutionary relationship than do proteins in the same superfamily. Sequence tools, such as BLAST, are used to assist in placing domains into superfamilies and families. The four families in the "Globin-like" superfamily of the "Globin-like" fold are displayed something like the following.
The families in SCOP may also be referred to using a SCOP concise classification string, sccs, which looks like, e.g., a.1.1.2 for the "Globin" family. The letter identifies the class to which the domain belongs; the following integers identify the fold, superfamily, and family, respectively.
Within a family are protein domains. Proteins are placed in the same protein domain if they are isoforms of each other, or if they are essentially the same protein, but from different species. This is apparently done manually. The "protein domains" are further subdivided into species. ("Protein domains" are not on separate pages in the current release of SCOP; in pre-SCOP, they are on separate pages.) Here is how some of the 81 protein domains of the "Globins" family are displayed.
The "TaxId" is the taxonomy ID number; it is also a link to the NCBI taxonomy browser, which provides more information about the species to which the protein belongs.
Clicking on a species or isoform brings up a list of domains. Here is how some of the 192 domains of the "Hemoglobin, alpha-chain from Human (Homo sapiens)" protein are displayed.
Clicking on the PDB numbers is supposed to display the structure of the molecule, but the links are currently broken. (The links do work in pre-SCOP.)
Most pages in SCOP contain a search box. Entering "trypsin +human" retrieves several proteins, including the protein trypsinogen from humans. Selecting that entry displays a page that includes the "lineage", which is at the top of most SCOP pages. The page includes the following information.
Searching for "Subtilisin" brings up the protein, "Subtilisin from Bacillus subtilis, carlsberg", with the following lineage.
Although both of these proteins are proteases, they do not even belong to the same fold, which is consistent with them being an example of convergent evolution.
This classification is more significantly based on the human expertise than semi-automatic CATH, its chief rival. Human expertise is needed to decide whether certain proteins are evolutionary related and therefore should be assigned to the same superfamily, or their similarity is a result of structural constraints and therefore they belong to the same fold. Another database, FSSP, is purely automatically generated (including regular automatic updates) but offers no classification, allowing the user to draw their own conclusion as to the significance of structural relationships based on the pairwise comparisons of individual protein structures.
To insert a link in Wikipedia to a particular SCOP page, use the template of the form {{SCOP|xxxxxx}}, where xxxxxx is a SCOP sunid, for instance SCOP 46456.
HOT DESIGNS ▪ Premium designs ▪ Designs by country ▪ Designs by U.S. state ▪ Most popular designs ▪ Newest, last added designs ▪ Unique designs ▪ Cheap, budget designs ▪ Design super sale DESIGNS BY THEME ▪ Accounting, audit designs ▪ Adult, sex designs ▪ African designs ▪ American, U.S. designs ▪ Animals, birds, pets designs ▪ Agricultural, farming designs ▪ Architecture, building designs ▪ Army, navy, military designs ▪ Audio & video designs ▪ Automobiles, car designs ▪ Books, e-book designs ▪ Beauty salon, SPA designs ▪ Black, dark designs ▪ Business, corporate designs ▪ Charity, donation designs ▪ Cinema, movie, film designs ▪ Computer, hardware designs ▪ Celebrity, star fan designs ▪ Children, family designs ▪ Christmas, New Year's designs ▪ Green, St. Patrick designs ▪ Dating, matchmaking designs ▪ Design studio, creative designs ▪ Educational, student designs ▪ Electronics designs ▪ Entertainment, fun designs ▪ Fashion, wear designs ▪ Finance, financial designs ▪ Fishing & hunting designs ▪ Flowers, floral shop designs ▪ Food, nutrition designs ▪ Football, soccer designs ▪ Gambling, casino designs ▪ Games, gaming designs ▪ Gifts, gift designs ▪ Halloween, carnival designs ▪ Hotel, resort designs ▪ Industry, industrial designs ▪ Insurance, insurer designs ▪ Interior, furniture designs ▪ International designs ▪ Internet technology designs ▪ Jewelry, jewellery designs ▪ Job & employment designs ▪ Landscaping, garden designs ▪ Law, juridical, legal designs ▪ Love, romantic designs ▪ Marketing designs ▪ Media, radio, TV designs ▪ Medicine, health care designs ▪ Mortgage, loan designs ▪ Music, musical designs ▪ Night club, dancing designs ▪ Photography, photo designs ▪ Personal, individual designs ▪ Politics, political designs ▪ Real estate, realty designs ▪ Religious, church designs ▪ Restaurant, cafe designs ▪ Retirement, pension designs ▪ Science, scientific designs ▪ Sea, ocean, river designs ▪ Security, protection designs ▪ Social, cultural designs ▪ Spirit, meditational designs ▪ Software designs ▪ Sports, sporting designs ▪ Telecommunication designs ▪ Travel, vacation designs ▪ Transport, logistic designs ▪ Web hosting designs ▪ Wedding, marriage designs ▪ White, light designs E-COMMERCE DESIGNS ▪ Magento store designs ▪ OpenCart store designs ▪ PrestaShop store designs ▪ CRE Loaded store designs ▪ Jigoshop store designs ▪ VirtueMart store designs ▪ osCommerce store designs ▪ Zen Cart store designs CMS DESIGNS ▪ Flash CMS designs ▪ Joomla CMS designs ▪ Mambo CMS designs ▪ Drupal CMS designs ▪ WordPress blog designs ▪ Forum designs ▪ phpBB forum designs ▪ PHP-Nuke portal designs ANIMATED WEBSITE DESIGNS ▪ Flash CMS designs ▪ Silverlight animated designs ▪ Silverlight intro designs ▪ Flash animated designs ▪ Flash intro designs ▪ XML Flash designs ▪ Flash 8 animated designs ▪ Dynamic Flash designs ▪ Flash animated photo albums ▪ Dynamic Swish designs ▪ Swish animated designs ▪ jQuery animated designs WEBSITE DESIGNS ▪ WebMatrix Razor designs ▪ HTML 5 designs ▪ Web 2.0 designs ▪ 3-color variation designs ▪ 3D, three-dimensional designs ▪ Artwork, illustrated designs ▪ Clean, simple designs ▪ CSS based website designs ▪ Full design packages ▪ Full ready websites ▪ Portal designs ▪ Stretched, full screen designs ▪ Universal, neutral designs CORPORATE ID DESIGNS ▪ Corporate identity sets ▪ Logo layouts, logo designs ▪ Logotype sets, logo packs ▪ PowerPoint, PTT designs ▪ Facebook themes VIDEO, SOUND & MUSIC ▪ Video e-cards ▪ After Effects video intros ▪ Special video effects ▪ Music tracks, music loops ▪ Stock music bank GRAPHICS & CLIPART ▪ Pro clipart & illustrations, $19/year ▪ 5,000+ icons by subscription ▪ Icons, pictograms |
| Super Offers |
| Super Offers |
| Custom Logo Design $149 ▪ Web Programming ▪ ID Card Printing ▪ Best Web Hosting ▪ eCommerce Software ▪ Add Your Link |
| © 1996-2013 MAGIA Internet Studio ▪ About ▪ Portfolio ▪ Photo on Demand ▪ Hosting ▪ Advertise ▪ Sitemap ▪ Privacy ▪ Maria Online
|
