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EROP-Moscow Help Page
Endogenous Regulatory OligoPeptide knowledgebase
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HELP CONTENT:
Introduction
Query Page
   EROP-accession
   Oligopeptide name
   karyote
   empire/kingdom
   phylum
   class/division
   organism
   taxon
   organ/secreted
   amino acid sequence
   abbreviations
   amino acid number
   molecular mass
   pI
   functional class
   function, key word(s)
   author
   title
   journal/book
   year
   author country
Result Page
Peptide Page
Family Page
Statistics Page
   First publication year
   Sequence size
   Biodiversity
   Amino acid composition
   Biological species
   Literature sources
   Countries
   Functional class
   Organ/tissue
   Author
Miscellaneous

Introduction

Here we present the compact specialized database EROP-Moscow (Endogenous Regulatory OligoPeptides) to provide a comprehensive description of all presently known natural oligopeptides. This database should now enable investigators to search easily for oligopeptides via a wide variety of different features, to compare their properties quickly, and to retrieve statistics about all relevant information in the database.
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Query Page

The Query page, entered from Home page via the "Query page" button, provides a rapid search for the peptide records signaled by specific characteristics. These characteristics are subdivided into the following groups: general information (such as oligopeptide name or EROP-Moscow accession number), organismic classification (including multiple trivial species names), physicochemical properties (such as partial amino acid sequences), biochemical or biologic functions, and literature references. Query examples (single words, phrases, or numbers) are provided adjacent to each Query window, and pull-down menus are provided with most query options. An "Abbreviations" button, located near the Query window for amino acid sequence, elicits display of the standard one-letter code for amino acid residues, along with optional abbreviations.

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   EROP-accession

Each entry is tagged by a unique accession number, beginning with character "E" (from EROP) followed by five numerical digits.

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   Oligopeptide name

Oligopeptide may have several names. One of them is used as the main, the others are given as synonyms.

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   karyote

Pull-down menu is provided to choose one from different karyotes. Akaryote term is used for viruses.

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   empire/kingdom

Pull-down menu is provided to choose one from different empires (or kingdoms).

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   phylum

Pull-down menu is provided to choose one from different phyla.

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   class/division

Pull-down menu is provided to choose one from different classes (or divisions).

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   organism

Hand input must be performed using an example adjacent "organism" Query window.

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   taxon

Hand input must be performed using an example adjacent "taxon" Query window.

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   organ/secreted

Hand input must be performed using an example adjacent "organ/secretion" Query window.

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   amino acid sequence

It' necessary to use standard one-letter code for amino acid residues for query.

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   abbreviations

The optional "Abbreviation" button adjacent "amino acid sequence" Query window permits to see these abbreviations.

AMINO ACID RESIDUE AND OTHER ABBREVIATIONS

standard amino acid residues:

A: alanyl, Ala
C: cysteinyl, Cys
D: aspartyl, Asp
E: glutamyl, Glu
F: phenylalanyl, Phe
G: glycyl, Gly
H: hystidinyl, His
I: isoleucyl, Ile
K: lysyl, Lys
L: leucyl, Leu
M: methionyl, Met
N: asparaginyl, Asn
P: prolyl, Pro
Q: glutaminyl, Gln
R: arginyl, Arg
S: seryl, Ser
T: threonyl, Thr
V: valyl, Val
W: tryptophanyl, Trp
Y: tyrosyl, Tyr

Because some oligopeptides are chemically modified at the N- and C-termini, six more symbols augment the standard one-letter code. These are:

+: to denote +H2, which is the open N-terminus
b: for an acetyl residue or other chemical group at the N-terminus
-: to denote O-, which is the open C-terminus
z: for an amide bond at the C-terminus
J: to denote the pyroglutaminyl linkage, formed by an N-terminal glutamine, due to side-chain reaction with the terminal amine residue
U: for the (occasional) aminoisobutyric acid residue.

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   amino acid number

Hand input can be performed using numbers from 2 to 50 (see an example adjacent Query window).

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   molecular mass

Hand input can be performed using values from approx. 100 to approx. 7000 with decimals (see an example adjacent Query window).

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   pI

Hand input can be performed using values from approx. 3 to approx 12 with decimals (see an example adjacent Query window).

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   functional class

Hand input can be performed using any common biochemical or biologic terms (see an example adjacent Query window).

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   function, key word(s)

Hand input can be performed using any words (see an example adjacent Query window).

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   author

Hand input can be performed using family name and inicials after family name without points (see an example adjacent Query window).

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   title

Hand input can be performed using any number of words.

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   journal/book

Hand input can be performed using one or more journal/book title words (see an example adjacent Query window)

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   year

Hand input can be performed using one year data from 1900 to current year.

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   author country

Pull-down menu is provided to choose one from different countries.

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Result Page

After entering a search word or phrase on the Query page, the user should click on the "Submit query" button, which initiates the search and returns with the Result page, containing a list of oligopeptides that meet the specified characteristics. Each item in this list will contain the preferred name of oligopeptide, the trivial and taxonomic names of organisms where the peptide has been identified, and the accession number. The accession number, in turn, links to the appropriate Peptide page (record). When the query returns only a single oligopeptide, its record opens immediately.

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Peptide Page

Peptide page, reached via accession number, presents the collected data on each oligopeptide, including the number of amino acid residues, primary structure, precursors, known posttranslational modification(s), affinity to any definite structure-function family, taxon(s) of biological sources, tissue/cell localization in each organism, major known biological functions, molecular mass (Da), isoelectric point, pI (calculated and experimentally observed), literature sources, and linking accession numbers (if any) in other peptide-protein databases or PubMed.

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Family Page

Tentative homologous family assignments, for each oligopeptide in EROP-Moscow, have been developed by sequence alignment, and the entire family on the Family page can be reached from the Peptide page via a "View family" button. Equally located amino acid residues are highlighted in red and the attached oligopeptide name for each sequence links back to the appropriate Peptide page.

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Statistics Page

A special set of pages is devoted to the overall characteristics of data on oligopeptides listed in EROP-Moscow. The starting Statistics page is reached from Home page via the "EROP Statistics" button, and it contains the list of statistical parameters compiled, each named parameter being a link to one of 15 additional Statistics pages (p.p. 1 - 10.2). These in turn present graphic and tabular information on oligopeptides currently available in EROP-Moscow.

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   First publication year

First publication year page shows a chronological diagram, by years, for decoding chemical structures of new oligopeptides (Statistics page 1).

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   Sequence size

Sequence size page shows size distribution of oligopeptides (number of amino acid residues) - Statistics page 2.

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   Biodiversity

Biodiversity page shows current numerical yield of oligopeptides per taxonomic group - Statistics page 3.

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   Amino acid composition

amino acid composition pade shows total amino acid residue content of all listed oligopeptides - Statistics page 4.

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   Biological species

Biological species pages show organisms covered - Statistics page 5.1 (ranged) and Statistics page 5.2 (alphabetical).

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   Literature sources

Literature sources pages show primary literature sources - Statistics page 6.1 (ranged) and statistics page 6.2 (alphabetical).

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   Countries

Country page shows relative contributions of international scientists, by home country, to the discovery of new oligopeptide structures - Statistics page 7.

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   Functional class

Functional classes pages show functional classes of oligopeptides - Statistics page 8.1 (ranged) and Statistics page 8.2 (alphabetical).

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   Organ/tissue

Organ/tissue pages show organ or tissues covered - Statistics page 9.1 (ranged) and Statistics page 9.2 (alphabetical).

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   Author

Authors pages show authors of the original publications devoted to decoding of oligopeptide chemical structures - Statistics page 10.1 (ranged) and Statistics page 10.2 (alphabetical).

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Miscellaneous

Some additional information and comments can be supplyied with Peptide page.

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SwissProt PIR PDB PubMed