HORDB a comprehensive database of peptide hormones

Peptide hormones (also known as hormone peptides and polypeptide hormones) are hormones composed of peptides and are signal transduction molecules produced by a class of multicellular organisms. It plays an important role in the physiological and behavioral regulation of animals and humans as well as in the growth of plants. In order to promote the research on peptide hormones, we constructed HORDB database. The database currently has a total of 6024 entries, including 5729 peptide hormones, 40 peptide drugs and 255 marketed pharmaceutical preparations information. Each entry provided comprehensive information related to the peptide, including general information, sequence, activity, structure, physical information and literature information. We also added information on IC50, EC50, ED50, target, and whether or not the blood-brain barrier was crossed to the activity information note. In addition, HORDB integrates search and sequence analysis to facilitate user browsing and data analysis. We believe that the peptide hormones information collected by HORDB will promote the design and discovery of peptide hormones, All data are hosted and available in figshare https://doi.org/10.6084/m9.figshare.c.5522241. Measurement(s) peptide hormone Technology Type(s) Comprehensive data website service Factor Type(s) peptide hormone Measurement(s) peptide hormone Technology Type(s) Comprehensive data website service Factor Type(s) peptide hormone


Background & Summary
Since the appearance of insulin therapy in the 1920s, peptide have played an important role in the medical field 1 . One advantage of peptide drugs is that they are highly specific, have low levels of toxicity and provide a variety of drug targets 2,3 . Nowadays, more than 60 peptide drugs have been approved for marketing, and over 150 peptides enter the clinical stage 1 .
Peptide hormones as therapeutic drugs have been widely used in the medical field. For example, exenatide is a synthetic glucagon like peptide-1 (GLP-1) analogue exendin-4, which consists of 30 amino acids 4,5 . Studies have shown that exenatide is superior to metformin in reducing weight, controlling blood sugar, improving liver enzymes and weakening NAFLD in T2DM patients with NAFLD 6,7 . Thymosin α 1 is a peptide composed of 28 amino acids, which has the functions of improving cellular immune function and regulating various immune functions. ZADAXIN, a drug developed by thymosin alpha 1, is approved in 35 countries for the treatment of viral infections, immunodeficiency, malignancies, and HIV/AIDS 8,9 . In recent years, due to the great progress in the detection and quantification of peptides in biological matrices, the information about peptide hormones has increased dramatically. Large amounts of data is scattered, and it is difficult to access it centrally. There are many databases related to peptide (such as DRAMP 10 , CancerPPD 11 , APD 12 , CAMP R3 13 etc.). These databases are used to store data on antimicrobial and anticancer peptides, but few databases on peptide hormones. As far as we know, Hmrbase 14 is a database specializing in hormones and receptors, but the data have not been updated since 2009. AHD 2.0 12 is the Arabidopsis thaliana plant hormone database, which does not contain peptide hormones data. In order to devote ourselves to the development of peptide hormones, we have built HORDB. As a comprehensive database of peptide hormones, HORDB not only collects the latest reported peptide hormones, but also comes from a wider range of sources. Such as from plants, animals, especially humans. Each entry consists of six categories: basic information, sequence, structure, activity, physics and documents. The database also includes information about peptide hormones in the market. We believe that with the development of artificial intelligence in peptide design, the data sets provided by HORDB will make it easier for researchers to develop prediction models of peptide hormones and accelerate the discovery of peptide hormones.
HORDB is an open user-friendly database. Includes two main data sets, peptide hormones and peptide hormones drug data set. Users can obtain peptide or drug information through simple, advanced search or browsing. The collection of sequence analysis tools facilitates the comparison of peptides with known sequences. www.nature.com/scientificdata www.nature.com/scientificdata/ HORDB covers a wide range, including plants, animals and humans, with rich information types, which is helpful for the development and utilization of peptide hormones. We have chosen the CC0 1.0 license and shared the data of HORDB with researchers. HORDB is available freely for public from http://hordb.cpu-bioinfor.org.

Methods
Data collection and compilation. The peptide hormones of HORDB are collected from PubMed, Google Scholar, UniProt 15 and PDB 16 by using keywords such as "hormone" and "peptide hormones". These matches are registered in the database if the following conditions are met: (1) the known amino acid sequence of the peptide; (2) the length is less than 100 amino acids; (3) mature peptide sequence without the precursor and signal regions; (4) a function annotation as hormone or phytohormone from literature or database such as UniProt or PDB. The information of peptide hormones drugs extracted from the literature and DrugBank 17 in accordance with the above requirements. Except for the calculation of physical and chemical parameters using SciDBMaker 18 , the rest of the information (like activity, 3-dimensional structure, sequence, etc.) is collected from literature and databases such as PDB 16 , Uni-Prot 15 , AlphaFold DB 19 , etc.

Database construction. The HORDB database is established on the standard platform of
Linux-Apache-MySQL-PHP (LAMP) with Linux as the operating system, Apache(version 2.2.22) as the server, MySQL server (version 5.5.29) as data management. HTML, PHP and JavaScript are applied to develop the front-end web interface. The architecture of HORDB database is given in Fig. 1.

Data Records
Peptide information. information about peptide hormones is obtained manually from different sources.
Each entry contains six parts: general information (ID, UniProt ID, protein name, gene name, source, family, disease, comments, external link), sequence information (sequence, length, pro-peptide, signal peptide, modification), activity (function, mechanism, target, IC 50 /EC 50 /ED 50 , cross BBB), Structure, physical information, literature (PubMed ID, title). In order to make the page more user-friendly, users can jump to related notes by clicking on the left navigation bar. Among them, the function information is the physiological function of the peptide hormones in the organism. The information in the structure information includes the 3-dimensional structure; The disulfide bond position point information indicates the existence of a disulfide bond at two amino acid positions by marking them. As shown in Fig. 2.
Drug information. The drug information includes the following fields: ID, active ingredients, DrugBank Accession Number, Active Sequence, Sequence Length, Type, Description, Disease, CAS, Drug. The drug field embodies the drugs that the protein has been on the market: drug name, strength dosage form/route, company marketing status, Drug ID, approval year. Among them, the types of drugs are divided into small molecule drugs and biosynthetic drugs. The peptide hormones drug information collected in this database mainly comes from the DrugBank database and literature reports. The drug information is shown in Fig. 3. According to their functions, these drugs are manually sorted and analyzed manually. They can be divided into calcium regulators, blood sugar regulation, anti-inflammatory effects, antidiuretic effects, somatostatin-like activity, intestinal regulation, vasoconstriction, reproductive regulation and others, among others. The category includes reducing fat accumulation and dilating blood vessels. As shown in Fig. 4. www.nature.com/scientificdata www.nature.com/scientificdata/ According to statistics, the HORDB database has a total of 6024 entries, including 5729 peptide hormones, 40 peptide drugs and and 255 marketed pharmaceutical preparations information. There were 408 three-dimensional structure files of peptide hormones from the PDB 16 (54 structures) and the AlphaFold DB 19 (354 files), respectively. The statistical results of the main information entries are shown in the Fig. 5.
All of our data sets were stored as tables, compressed packages, and text in figshare 20 . "Peptide structure. zip" and "Peptide sequence.fasta.txt" for peptide structure (.pdb) and sequence information file (.fasta), respectively. Other excel files are used to store various kinds of information of peptide hormones, such as "Peptide hormones infomation.xlsx" used to store information of peptide hormones such as name, organization, source, activity, expression, structure, and so on; "Peptide Physical Information.xlsx" used to store information of physicochemical properties of peptide hormones. "Peptide Hormones Drugs Information.xlsx" and "Marketed Pharmaceuticals preparations infomation.xlsx" are used to store information on peptide drugs and their www.nature.com/scientificdata www.nature.com/scientificdata/  www.nature.com/scientificdata www.nature.com/scientificdata/ preparations. At the same time can also through our online database website browsing, use, download data, we will regularly update the data. The website is http://hordb.cpu-bioinfor.org.
technical Validation Data validation. We manually proofread and validate the main data of HORDB at the back end of the website. For peptide hormones data, we re-validated the number of primary information entries based on the MySQL metadata information. Check the accuracy of information by random sampling. For the metadata of MySQL database, in order to facilitate researchers and subsequent data sorting and updating, it was divided into four data tables, namely, peptide information master data (hor_gen), active pep (Active_PEP), peptide physical data (hor_phs) and market drug preparation data. All datasets are available on the download page.
Data update. In addition to our regular updates, we also set up a submission page to encourage researchers to participate in HORDB data updates as contributors. Researchers can also give us any advice through the www.nature.com/scientificdata www.nature.com/scientificdata/  www.nature.com/scientificdata www.nature.com/scientificdata/ www.nature.com/scientificdata www.nature.com/scientificdata/ contact information on the homepage. With the deployment of the HORDB, we plan to update the data about every three months. In addition, when major changes that require version control occur, the production version of the database will be updated regularly.

Usage Notes
The homepage of HOROB contains the following interfaces: search, browse, tools, statistics, downloads and links. A brief description of the interface is given below, and a screenshot is given in Fig. 6.

Download.
We are willing to share our data with users, so the website is designed with a download interface.
The downloadable interface is divided into four parts: general information, physical information, peptide drug information, peptides sequence, peptide structure and listed drug information.
HORDB data statistics. The current version of the HORDB database contains 6,024 entries, including 5,729 peptide hormones, 40 peptide drugs, and 255 pharmaceutical preparations on the market. 408 peptide hormones had available three-dimensional structures; They are collected from the PDB 16 and AlphaFoldDB 19 . Among them, 28 peptide hormones could cross the blood-brain barrier; 22 peptide hormones with clear disease information. In order to improve the understanding of the characteristics of peptide hormones and serve as the basis for the design of peptide hormones, the peptide sequences in the database were analyzed and counted. In the database, most peptide were derived from animals, as shown in Fig. 7. According to the protein classification criteria of UniProt 15 , there are 80 families in the HORDB. The most abundant (856 in total) were the FMRFamide related www.nature.com/scientificdata www.nature.com/scientificdata/ peptide families, and the distribution of peptide hormones families is shown in Fig. 8. The peptide hormones shown in Fig. 9 is mostly positively char. Among the peptide with known sequences, most peptide are about 10 amino acids in length (as shown in Fig. 10). The results showed that short peptide formed peptide hormones more easily than long peptide. As shown in Fig. 11, the proportion of hydrophobic residues in most peptide is 20-40%, indicating that most peptide hormones in HORDB are less hydrophobic. The distribution of amino