Structural Classification of Proteins


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Structural Classification of Proteins (SCOP)

The SCOP database can be easily accessed freely on the internet. SCOP is generated from physical review and supported by a sequence of programmed techniques. Its goal is to offer exhaustive and an all-inclusive account of the fundamental and evolutionary connections among the different proteins whose structure is recognized. The SCOP database is a huge categorization of fundamental fields of the proteins on the nature of amino acid order likeness and 3-D structures. The fundamentally oriented SCOP database describes families containing of proteins with 30% resemblance, and proteins with inferior order identity though with comparable purpose and configuration (Reddy and Bourne 2003). In addition, SCOP also allocates proteins into superfamilies which create segments of distant homologs with possible lower order element than families. However, they tend to share similar ancillary structure in one order (Reddy and Bourne 2003).

The reason for this categorization is to establish the evolutionary correlation among the proteins. Proteins with similar shapes but possess little order or operational likenesses are positioned in various superfamilies, and are presumed to only have a not close shared ancestor. On the other hand, the proteins that possess similar and same order and/or operation are position in families and are considered to have a near common ancestor.

Levels of SCOP database

SCOP database has seven levels that comprise of:

  1. Class – This entails they forms of folds such as the beta sheets
  2. Fold – These entails the various shapes of domains contained in a given class
  3. Superfamily – The domains contained in the fold are segmented into superfamilies that tend to have a shared ancestor
  4. Family – Domains in the superfamily are segmented into families that have a shared ancestor that is quite recent
  5. Protein domain – The domains in families are segmented into protein domains that are mainly similar to the protein
  6. Types – The domain featured in protein domains are segmented as per the types
  7. Domain – Section of a protein. For basic proteins, it could be the complete protein.

The folds are categorized classes that are made up of top level, or root of the SCOP hierarchical categorization.


TreMBL which is also referred to as UniProtKB comprises of high quality computationally examined registers that are enhanced with programmed explanation. It was incepted in reaction to improved dataflow emanated from genome projects since the process of UniProtKB/Swiss-prot that was time and labor sensitive could not be expanded to comprise all the protein sequences that were available.

As noted by Boeckmann et al. (2003), TreMBL characterizes the Transformed EMBL Nucleotide Sequence Data Library and was incepted in the year 1996 and is considered to be the machine-programmed equivalent to SwissPort. According to Schneider et al. (2005), the objective of TrEMBL is to integrate the advancement in protein order output from genome ordering projects awaiting manual curation.

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MEROPS dataset

Merops is a database that is based online and is for peptidases (proteases) together with their inhibitors. This type of database can be expounded on as an information source for peptidases together with the proteins that constrain them. By using an index as per its Name, MEROPS Identified or Source Organism, the summary can be accessed. The summary defines the segmentation and nomenclature of the peptidase and provides connection to auxiliary pages indicating order identifiers, the structures if established, and literature references among others.

The MEROPS database applies a classified, structure-based categorization of the peptidases where each of the peptidase is allocated a filmily depending on major statistic likeness in the order of amino acids, while families that are perceived to be homologous are categorized together in a clan. There is a synopsis page for every family and clan which also has indexes.  Every synopsis page provides links to the auxiliary pages.


SWISS-PROT entails a curated protein classification database that aims to offer a high degree of annotation (For instance the account of the purpose of a protein, the main structure, post-translational adjustments, differences, etc.), a marginal level of redundancy and high level of incorporation with various databases. The SWISS-PORT database, that is commonly used for classification and other information on protein can be used online at and can also be assessed via the Expert Protein Analysis System (ExPASy; The ExPASY entails a resource portal of the Swiss Institute of Bioinformatics (SIB).

The version 2016_02 of 17-Feb-16 of UniProtKB/Swiss-Prot features 550552 order entries, entailing 196472675 amino acids obtained from 242331 references.


Interpro offers practical exploration of proteins by grouping them into families and anticipating domains and vital sites. It incorporates protein signatures from a variety of member databases into one resource that is searchable, focusing on the specific strengths to produce a powerful integrated database as well as a diagnosis mechanism.

InterPro incorporates different prognostic protein signatures from wide source repositories, for example, Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY, and TIGRFAMs. Protein signatures from different databases are incorporated into InterPro manually. Curators join signatures signifying similar protein family, domain, or site into a specific database entry, and where likely, trace biological relationships among the essential signatures (


OMIM is an acronym of Online Mendelian Inheritance in Man database. This type of database is an inclusive compendium of human genes and genetic-disease-linked phenotypes. The database is a persistently updated catalogue of human genes and genetic conditions and aspects, with specific concentration on the molecular correlation among genetic difference and phenotypic expression. It is therefore perceived to be a phenotypic acquaintance to the Human Genome Project. OMIM can also be expounded as an advancement of Dr. Victor A. McKusick’s Mendelian Inheritance in man that was made public through 12 editions with the last edition been in the year 1998. Presently, OMOM is biocurated atJohns Hopkins University School of Medicine and McKusick-Nathans Institute of Genetic Medicice.

By the end of July 2015, nearly 8,062 of the 23,000 entries in OMIM signified phenotypes while the others represented genes with most of them been lined to known phenotypes.


HUGO is an acronym of Human Genome Organization. The Hugo Gene Nomenclature (HGNC) entails a committee of HUGO that determines the standards for human gene nomenclature. HGNC supports a different and meaningful name for each known human gene as per the query of experts. Moreover, HGNC also allocates a symbol that comprises of a short group of characters to each gene. HGNC is mandated to agree different symbols and names pertaining to human loci, comprising of protein coding genes, RNA genes and pseudogenes, to permit unequivocal scientific interactions.