User guide
1. Introduction
Q-BioLiP is a database for biological unit-ligand interactions, as an improved version of the BioLiP. All data was collected from RSCB PDB initially.Other additional useful information was also collected,which are listed below
- PubMed: comprise millions of citations from various periodicals
- BindingMOAD, PDBbind-CN, BindingDB: record experimentally determined binding affinities of protein–ligand complexes, Most of them come from the primary references. The indicators mentioned include: Kd, Ki,and IC50.
2. Flowchart
3. Home page
The homepage provides a brief introduction of Q-BioLiP, a quick search by PDB ID, you can browse all of the entries.
4. Search
In search page, you can search by name: PDB ID,Uniprot ID,Ligand ID,Ligand Name. Or search by structure.
The search result by name:
The search result by structure:
In each entry page, you can get the detailed information.
5. Ligand
We collected detail information for each ligand in Q-BioLiP, In this page you can browse all ligands or search by Ligand ID or Ligand Name.
6. Binding affinity
The experimental binding affinity was collected from BindingDB,BindingMOAD,and PDBbind. Sometimes the exterimental data is missed, so we calculated scores by Vina,Mdock and X-Score. In PDBbind core dataset, we trained a linear regression model for each score. Q-BioLiP provided each score, the precicted score and 90% confidence interval. Additionaly,we trained a multiple linear regression based on the scores above.
Reference