Ligand Binding Site Prediction

Ligand binding is required for many proteins to function properly. A large number of bioinformatics tools have been developed to predict ligand binding sites as a first step in understanding a protein's function or facilitating docking computations in virtual screening-based drug design. Prediction usually only needs to search for the three-dimensional structure of the target protein of the ligand binding site (experimental determination or computational modeling) and the construction of a web server allows free and simple use of prediction tools. CD ComputaBio is proud to provide the most efficient protein-ligand binding site prediction services to our clients.

Protocol for Ligand Binding Site Prediction.Figure 1. Protocol for Ligand Binding Site Prediction. (Ambrish Roy.; et al,2012)

Overall solutions

  • Template-based: those that make use of homologous or similar structures with already known binding sites
  • Geometry-based: those that carry out some kind of geometric computation to identify binding site pockets
  • Energy-based: those that compute the interaction energy using imaginary ligands as binding probes
  • Propensity-based: those that compute the propensity of a certain property that indicates a statistically significant preference for known LBSs, rather than non-LBSs
  • Combination-based and others: those that perform the prediction based on the results of other methods and those that cannot be easily classified into one of the above categories

Our tools

Tools Functions
cons-PPISP A consensus neural network method for predicting interaction sites.
BAPPL computing binding free energy of a non-metallo protein-ligand complex using an all atom energy based empirical scoring function.
BAPPL-Z Binding affinity prediction of protein-ligand complex containing Zinc.
DrugScore Knowledge-based scoring functions. DrugScore enables you to score protein-ligand complexes of your interest and to visualize the per-atom score contributions.
FoldX Calculating binding energy.
PEARLS Computing small molecule ligand-protein, ligand-nucleic acid, protein-nucleic acid and ligand-protein-nucleic acid interaction energies.

Our services

Project name Ligand Binding Site Prediction
Samples requirement Our ligand binding site prediction requires you to provide specific requirements.
Timeline Decide according to your needs.
Deliverables We provide you with raw data and analysis service.
Price Inquiry

 Our advantages

  • CD ComputaBio use a variety of methods to provide you with ligand binding site predictions.
  • Short service period and high efficiency.
  • Nowadays, we can provide many tools and techniques are available to analyze the alignment product and provide the sequence comparisons to study its biology.

CD ComputaBio can offer you but not limited to:

Ligand Binding Site Prediction 2

CD ComputaBio provides corresponding ligand binding site prediction services. Our service provides result that it is very useful for understanding the biochemical basis of physiological events. Our expert team can choose the most suitable analysis method for you, so you don't have to worry about technical issues. The CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals.


  1. Ambrish Roy.; et al. Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement. Cell.2012.
* For Research Use Only.