CONTENTS
The browsing facility allows a user to explore the data for neuropeptides by major fields including (i) families of neuropeptides; (ii) organisms of neuropeptides; (iii) post-translational modifications, and allows a user to explore the data for neuropeptide receptors by fields including (i) organisms of neuropeptide receptors; (ii) post-translational modifications.
Quick Search
A quick search feature allows users to search the database for neuropeptides or neuropeptide receptor with keywords such as sequence, name, organism, and NPID, etc. The information of neuropeptide or receptor matching the query keywords are retrieved from the database and shown in a table format. User can download the table or the sequence in fasta format. User can also click on the ID URL link of neuropeptide or receptor which be interested in, the annotations about the neuropeptides or receptors will be showed.
This page allow users to access the detailed information on a single neuropeptide entry. The information in this page is divided into various sections.
Basic Information shows the basic information for a neuropeptide , which was extracted from different sources. Cross links were extracted from UniProt, PubMed, Taxonomy, STRING and AmiGO.
Click "Physicochemical Properties" to view the physicochemical properties of neuropeptide.
Physicochemical Properties show the physico-chemical properties, hydropathy and amino acids composition.
Click "Receptors" to view the receptor of neuropeptide.
Receptors show brief information of receptor if available. Receptors interacting with neuropeptide were extracted from UniProt, STRING, Guide to PHARMACOLOGY and GPCRdb.
The user can access the detailed information of receptor by click the NPRID.
Click "Structure" to view the structure of neuropeptide.
Structure shows the experiment structure or the predict the 3D structure of neuropeptide. Alphafold2 and APPTEST were used to predict the 3D structure of neuropeptide and neuropeptide receptor without experiment structure. The user can download the experiment structure or the predict the 3D structure by the download link.
Click "Complex structure " to view the complex structure of neuropeptide and receptor.
Complex structure shows the 3D structure of the complex of neuropeptide and receptor if available. The neuropeptide structure is shown as stick. The neuropeptide receptor structure is show as cartoon. The user can also download the complex structure by the download link.
An advanced search page helps users to combine search with logical operators like AND/OR to search the database. In addition, advanced search allows users to specify a search range. The information of neuropeptide or receptor matching the query keywords are retrieved from our database and shown in a table format. The following example shows extracting neuropeptides name of substance p with the length range of 10 to 50.
Blast
Blast is used to search for similar sequences against the neuropeptide database.
MAP is used to retrieve NeuroPep 2.0 database peptides against the query sequence.
DeepNeuropePred employs a combination of pre-trained language model and Convolutional Neural Networks for feature extraction, thereby predicting the neuropeptide cleavage sites from precursors.
NeuroPred-PLM employs a combination of pre-trained language model and attention mechanism to predict neuropeptides.
The submission page provides a window where users can submit their peptide or receptor data to this database.
