AlloBase Overview
AlloBase is a comprehensive database of allosteric regulation in proteins, integrating structural, functional, and clinical data across diverse protein families. This documentation provides complete information on how to access and utilize the database effectively.
Key Features
- 1,465 curated proteins across 15 protein families
- 36 allosteric drugs with clinical information
- 500 allosteric sites with detailed annotations
- 500 communication pathways mapping signal propagation
- 62 protein structures with experimental validation
- RESTful API for programmatic access
Getting Started
New users are recommended to:
- Read the Data Model section to understand the database structure
- Try the interactive browsing features
- Explore the search functionality for specific queries
- Test the API for programmatic access
- Check the tutorials for common use cases
Data Model & Schema
AlloBase follows a structured data model to ensure consistency and interoperability. The main entities and their relationships are described below.
Core Entities
Proteins
Protein entries include comprehensive information about sequence, structure, and function.
Key Fields: UniProt ID, Protein Name, Gene Name, Organism, Protein Family, Sequence Length, Functional Annotation
Allosteric Sites
Detailed characterization of allosteric binding sites with structural and functional annotations.
Key Fields: Site ID, Residue Numbers, Validation Methods, Experimental Evidence, Confidence Score, Publication PMID
Allosteric Drugs
Clinically relevant allosteric modulators with mechanism of action and therapeutic applications.
Key Fields: Drug Name, DrugBank ID, Clinical Status, Target Proteins, Mechanism, Indication, Approval Year
Communication Networks
Allosteric communication pathways mapping signal propagation through protein structures.
Key Fields: Network ID, Active Site Residues, Allosteric Site Residues, Pathway Residues, Communication Strength, Prediction Method
Protein Structures
Experimentally determined protein structures with allosteric annotations.
Key Fields: PDB ID, Resolution, Experimental Method, Structure Length, Allosteric Sites Count
Data Relationships
| Relationship |
Description |
Cardinality |
| Protein ↔ Allosteric Site |
One protein can have multiple allosteric sites |
1:N |
| Protein ↔ Drug |
Multiple drugs can target the same protein |
1:N |
| Protein ↔ Communication Network |
Each protein has defined allosteric communication pathways |
1:1 or 1:N |
| Protein ↔ Protein Structure |
Multiple structures available for each protein |
1:N |
Browsing Data
AlloBase provides multiple ways to explore the database content through intuitive browsing interfaces.
Protein Family Browser
Browse proteins organized by family classification:
- Kinases - Protein kinases with allosteric regulation
- GPCRs - G-protein coupled receptors
- Ion Channels - Voltage and ligand-gated channels
- Scaffold Proteins - Signaling scaffold proteins
- Chaperones - Molecular chaperones
Drug Browser
Explore allosteric drugs by therapeutic area and mechanism:
- By Therapeutic Area: Oncology, CNS, Metabolic, Cardiovascular
- By Mechanism: Allosteric Modulator, Allosteric Activator
- By Clinical Status: Approved, Clinical Trials, Preclinical
Structure Browser
Access experimentally determined structures with allosteric annotations:
Features: PDB structure information, Resolution data, Experimental methods, Allosteric site annotations
Searching AlloBase
Advanced search capabilities allow precise querying of the database.
Basic Search
The main search bar supports queries for:
- Protein names and gene symbols
- Drug names and identifiers
- Protein families and organisms
- Therapeutic areas and mechanisms
Advanced Search
Multi-criteria search with filters for:
Search Filters:
• Protein Properties: Family, Organism, Length Range
• Allosteric Sites: Validation Method, Confidence Score
• Drugs: Clinical Status, Mechanism, Therapeutic Area
• Structures: Resolution Range, Method (X-ray/Cryo-EM)
• Communication: Pathway Length, Communication Strength
Search Examples
Example 1: Find all allosteric drugs for kinases in clinical trials
Example 2: Identify proteins with experimentally validated allosteric sites
Example 3: Search for allosteric communication pathways with high communication strength
API Access
Programmatic access to AlloBase through RESTful API endpoints. All endpoints return JSON responses and support filtering parameters.
Base URL
http://localhost/allosdb/api.php
Authentication
All API endpoints are publicly accessible without authentication. For high-volume usage, please contact us.
Available Endpoints
GET
Proteins Endpoint
Retrieve protein information with optional filtering
// Get all proteins with limit
GET api.php?endpoint=proteins&limit=10
// Get proteins by family
GET api.php?endpoint=proteins&family=Scaffold Protein&limit=5
// Get specific protein by UniProt ID
GET api.php?endpoint=proteins&id=A0JLT2
// Available parameters:
?endpoint=proteins
&id=UNIPROT_ID (optional)
&family=FAMILY_NAME (optional)
&organism=ORGANISM (optional)
&limit=NUMBER (optional, default: 50, max: 100)
GET
Drugs Endpoint
Access allosteric drug data with clinical information
// Get all drugs with limit
GET api.php?endpoint=drugs&limit=10
// Get drugs by therapeutic area
GET api.php?endpoint=drugs&therapeutic_area=oncology
// Get drugs by clinical status
GET api.php?endpoint=drugs&clinical_status=approved&limit=5
// Get specific drug by DrugBank ID
GET api.php?endpoint=drugs&id=DB00281
// Available parameters:
?endpoint=drugs
&id=DRUGBANK_ID (optional)
&therapeutic_area=AREA (optional)
&clinical_status=STATUS (optional)
&limit=NUMBER (optional, default: 50, max: 100)
GET
Allosteric Sites Endpoint
Query allosteric binding sites with validation data
// Get all sites with limit
GET api.php?endpoint=sites&limit=10
// Get sites by validation method
GET api.php?endpoint=sites&validation=X-ray crystallography
// Get sites for specific protein
GET api.php?endpoint=sites&protein=P24941&limit=5
// Get specific site by ID
GET api.php?endpoint=sites&id=AS000001
// Available parameters:
?endpoint=sites
&id=SITE_ID (optional)
&validation=METHOD (optional)
&protein=UNIPROT_ID (optional)
&pdb_id=PDB_ID (optional)
&limit=NUMBER (optional, default: 50, max: 100)
GET
Communication Networks Endpoint
Retrieve allosteric communication pathway data
// Get all networks with limit
GET api.php?endpoint=networks&limit=10
// Get networks for specific protein
GET api.php?endpoint=networks&protein=P24941&limit=5
// Available parameters:
?endpoint=networks
&protein=UNIPROT_ID (optional)
&pdb_id=PDB_ID (optional)
&limit=NUMBER (optional, default: 50, max: 100)
GET
Protein Structures Endpoint
Access protein structure data with allosteric annotations
// Get all structures with limit
GET api.php?endpoint=structures&limit=10
// Get structures for specific protein
GET api.php?endpoint=structures&protein=P00742&limit=5
// Available parameters:
?endpoint=structures
&protein=UNIPROT_ID (optional)
&method=EXPERIMENTAL_METHOD (optional)
&limit=NUMBER (optional, default: 50, max: 100)
Response Format
All API responses follow a consistent JSON structure:
{
"status": "success",
"data": [
{
"uniprot_id": "A0JLT2",
"protein_name": "Mediator of RNA polymerase II...",
// ... other fields
}
],
"count": 1,
"timestamp": "2025-11-15T04:46:18+00:00"
}
Error Responses
Error responses include descriptive messages and HTTP status codes:
{
"status": "error",
"message": "Protein not found: INVALID_ID",
"timestamp": "2025-11-15T04:46:18+00:00"
}
Usage Examples
JavaScript Example
// Fetch proteins from AlloBase API
async function fetchProteins(family = '', limit = 10) {
const url = `api.php?endpoint=proteins&limit=${limit}&family=${family}`;
const response = await fetch(url);
const data = await response.json();
if (data.status === 'success') {
return data.data;
} else {
console.error('API Error:', data.message);
return [];
}
}
// Usage
const kinases = await fetchProteins('Kinase', 5);
console.log(kinases);
Python Example
import requests
import json
# Fetch allosteric sites data
def fetch_allosteric_sites(protein_id=None, limit=10):
params = {
'endpoint': 'sites',
'limit': limit
}
if protein_id:
params['protein'] = protein_id
response = requests.get('http://localhost/allosdb/api.php', params=params)
data = response.json()
if data['status'] == 'success':
return data['data']
else:
print(f"Error: {data['message']}")
return []
# Usage
sites = fetch_allosteric_sites(protein_id='P24941', limit=5)
print(f"Found {len(sites)} allosteric sites")
Live API Test
Test the API endpoints directly using our interactive test interface:
Tutorials & Use Cases
Step-by-step guides for common research scenarios.
Tutorial 1: Identifying Novel Allosteric Targets
Learn how to use AlloBase to identify potential allosteric targets for drug discovery:
- Start with protein family of interest using the browse interface
- Filter by existing allosteric site annotations
- Analyze communication networks for key residues
- Check available structural data
- Export results for further analysis
Tutorial 2: Drug Repurposing Analysis
Identify existing drugs that could target new allosteric sites:
- Search for drugs by mechanism and clinical status
- Analyze target proteins and their families
- Compare allosteric site characteristics
- Check communication pathway similarities
Tutorial 3: Integrating AlloBase with Computational Tools
Use API access to integrate AlloBase data with molecular modeling pipelines:
# Python example: Fetch protein data for molecular dynamics
import requests
# Get protein data
response = requests.get('http://localhost/allosdb/api.php?endpoint=proteins&id=P24941')
protein_data = response.json()
# Get allosteric sites for this protein
sites_response = requests.get('http://localhost/allosdb/api.php?endpoint=sites&protein=P24941')
sites_data = sites_response.json()
# Use in analysis pipeline
if sites_data['status'] == 'success':
for site in sites_data['data']:
print(f"Site: {site['site_id']}, Residues: {site['residues']}")
print(f"Validation: {site['validation_method']}, Confidence: {site['confidence_score']}")
Frequently Asked Questions
Data Questions
Q: How often is AlloBase updated?
A: AlloBase is updated quarterly with new data from literature curation and computational predictions.
Q: Can I submit my own data to AlloBase?
A: Yes, we welcome data submissions. Please use our data submission form or contact us directly.
Technical Questions
Q: Is there a limit on API requests?
A: The public API is freely accessible. For high-volume usage, please contact us for coordination.
Q: Can I download the entire database?
A: Yes, complete datasets are available in the download section in multiple formats.
Usage Questions
Q: Is AlloBase free for academic use?
A: Yes, AlloBase is freely available for academic and non-commercial research.
Q: How do I report errors in the data?
A: Please use the feedback form or email errors@allobase.org.
Q: What browsers are supported?
A: AlloBase works with modern browsers including Chrome, Firefox, Safari, and Edge.