Website Guide and Real-Use Workflows
Pep2Net-DB is a curated peptide knowledgebase for exploring peptide sequences, assay-level evidence, biological functions, source information, structural annotations, predictive models, and reusable data packages. This page starts from common research tasks, then provides a complete module overview for users who want to understand the whole website.
Quick Start: Start from the Research Task
These tasks are organized around what users usually want to accomplish, not around one page at a time. Each guide may combine Search, Browse, Tools, Statistics, and Download when that is the more natural route.
Task 1. Check what is known about a peptide or keyword
Use this route when you already have a peptide name, peptide ID, organism, function label, publication identifier, patent number, assay method, or another keyword. Start broad, then add filters only if the result set is too large.
- Try the known term in the Home search box for a fast first lookup.
- Use Advanced Search when several conditions are known, such as function plus source, evidence status, property range, or structure availability.
- Open matched records to review sequence, function, source, assay context, and literature or patent evidence.
Task 2. Assess a new peptide sequence
Use this route when you have a peptide sequence and want to know whether similar peptides already exist, whether related records contain useful evidence, or whether prediction models can provide additional descriptors or activity estimates.
- Paste the amino-acid sequence into Sequence Similarity and run the search.
- Adjust identity, length tolerance, result count, or optional filters if the result list is too broad or too narrow.
- Review the closest records for known function, source, assay evidence, and structure availability.
- Use Tools to calculate descriptors or run prediction models for the sequence when database evidence is limited or additional analysis is needed.
Task 3. Find evidence-supported candidates for a function or source
Use this route when the goal is not one known peptide, but a group of candidate peptides: for example antibacterial peptides, peptides from a source organism, peptides active against a target organism, or peptides belonging to a broader functional class.
- Use Function Browse or Source Browse to understand available categories and select the most relevant class.
- Use Advanced Search when you need to combine function, source, target organism, property range, evidence status, or structure availability.
- Use Assay Record Browse to compare activity-related evidence before treating a peptide as a candidate.
Task 4. Review whether a peptide has reliable activity evidence
Use this route when the experimental record matters more than the sequence list itself. This is useful before citing a peptide, selecting candidates for validation, or comparing activity under different assay conditions.
- Search by sequence, peptide name, function, or assay-related terms when available.
- Compare target organism, activity value, assay method, PMID, patent number, review status, and standard status.
- Open the linked peptide record to connect assay evidence with sequence, source, function, and structure information.
Task 5. Prepare a non-redundant sequence set
Use this route when you want one entry per peptide sequence before comparison, screening, modelling, or downstream analysis. This avoids treating repeated assay observations as separate sequence entries.
- Use Unique Sequence Browse to work at the deduplicated sequence level.
- Filter by sequence text, peptide length, reviewed status, or standard status.
- Open sequence-level records for annotation context, or use Download when a reusable dataset package is needed.
Task 6. Use structure to find related peptides
Use this route when structural resemblance is more important than exact sequence similarity. It is suitable when a peptide has known structural information or when you have a PDB file for comparison.
- Choose a database peptide ID with structure information or upload a PDB file.
- Set the minimum score, result count, candidate retrieval depth, and optional biological filters.
- Inspect ranked matches and open linked records to review function, source, assay evidence, and sequence context.
Task 7. Understand database coverage or export data
Use this route before larger analysis work. Statistics helps you judge database composition, while Download provides reusable files for local analysis, sequence workflows, evidence review, or metadata reuse.
- Use Statistics to inspect database scale, sequence properties, function distribution, evidence patterns, and source composition.
- Use Download to choose recommended packages, function-focused collections, source-focused collections, assay evidence sets, chemistry and structure packages, or metadata files.
- Select the format that matches the downstream task, such as CSV, FASTA, or JSON.
Site Overview
Use this part when you want to understand the whole website. The sections below keep the module-based structure and include the relevant screenshots used in the task guides.
- Home introduces the database, global search, navigation, statistics highlights, and pipeline context.
- Search supports field-based retrieval, sequence similarity, and structure similarity.
- Browse supports category-driven exploration by peptide type, function, source, unique sequence, and assay record.
- Tools provides descriptor calculation and prediction utilities for user-submitted peptide sequences.
- Statistics summarizes database composition and distribution patterns.
- Download provides reusable datasets and selected metadata packages.
1. Home Page
The Home page is the main entry point for Pep2Net-DB. It introduces the curated peptide knowledgebase, supports global keyword search, and points visitors toward the main website modules.
1.1 Top Navigation Bar
- Search
- Opens Advanced Search, Sequence Similarity, and Structure Similarity for targeted retrieval and comparison.
- Browse
- Provides curated entry points by peptide type, function ontology, source organism, unique sequence, and assay record.
- Tools
- Leads to peptide prediction utilities for physicochemical properties, structure-related descriptors, and biological activities.
- Statistics
- Summarizes database composition, sequence properties, functional distributions, evidence patterns, and source information.
- Download
- Provides reusable CSV, FASTA, JSON, evidence, structure, and metadata packages.
1.2 Home Search Box
The large search box in the hero area supports broad keyword retrieval. Users can enter biological terms, identifiers, source or target organisms, function labels, publication identifiers, or known peptide names. After searching, matching peptide or assay records can be explored in more detail.
1.3 Related Home Sections
Below the hero search area, the Home page highlights database scale, access routes, output options, and the data integration pipeline. These sections help new visitors understand what the database contains and which module should be used next.
2. Search Page
The Search module supports three complementary modes: field-based advanced search, sequence similarity search, and structure similarity search.
2.1 Advanced Search
Advanced Search provides structured filters for peptide fields, assay context, physicochemical properties, evidence status, and structure availability. It is most useful when users already know several conditions and need a controlled result set.
2.2 Sequence Similarity
Sequence Similarity compares a query amino-acid sequence against database peptides. Users can adjust identity, length tolerance, maximum result count, and optional biological filters before reviewing ranked matches.
2.3 Structure Similarity
Structure Similarity searches peptide structural similarity using an existing peptide ID with structure information or an uploaded PDB file. It helps users identify peptides with related three-dimensional patterns or comparable structural signatures.
3. Browse Page
Use Browse when you want to scan peptide categories, compare functional classes, inspect biological sources, review unique sequences, or work directly with assay-level records.
3.1 Peptide Type
The Peptide Type page groups records by structural type and chirality. Tables and charts summarize category counts, and users can select a row or chart segment to open the matching record list.
3.2 Function
The Function page displays a biological function ontology. Visitors can search within function names and paths, expand or collapse the ontology tree, view peptide counts beside each class, and open category-specific result pages.
3.3 Source
The Source page summarizes peptides by biological or design origin, such as animal, bacterium, plant, fungus, virus, synthetic, and other source classes. It provides source cards and a source distribution chart for quick comparison.
3.4 Unique Sequence
The Unique Sequence page focuses on deduplicated peptide sequences. It is useful when visitors want sequence-level records rather than repeated assay observations. Search and filter controls help narrow the list by sequence text, reviewed status, standard status, and peptide length.
3.5 Assay Record
The Assay Record page presents activity evidence at the record level. It includes peptide sequence search, reviewed-status filters, standard-status filters, length filters, and a table containing record ID, name, sequence, source organism, function category, target organism, activity, assay method, PMID, patent number, and review status.
4. Tools Page
The Tools entry point is the Peptide Property Predictor. Users can enter one or more peptide sequences, select prediction models, and submit the job to receive model-based predictions and computed peptide descriptors.
Use this module when the peptide sequence is already available and the next task is prediction rather than database retrieval. The page supports descriptor calculation and selected biological activity models, including physicochemical, structure-related, antibacterial, antiviral, toxicity, therapeutic, antifungal, and other function groups when available.
5. Statistics Page
Statistics helps visitors understand the overall composition of Pep2Net-DB before they browse, search, or download data.
Use Statistics to inspect database scale, sequence properties, function distribution, evidence landscape, source patterns, and other summary views. This is useful before deciding which subset of the database should be searched, reviewed, or exported.
6. Download Page
Download provides reusable files for analysis outside the website, including recommended packages, function-focused collections, source-focused collections, assay evidence sets, chemistry and structure packages, and metadata files.
Available formats include CSV for tabular analysis, FASTA for sequence workflows, and JSON for selected evidence or metadata resources.