Cloud Computing for Protein-Ligand Binding Site Comparison

Abstract EN

The proteome-wide analysis of protein-ligand binding sites and their interactions with ligands is important in structure-based drug design and in understanding ligand cross reactivity and toxicity.

The well-known and commonly used software, SMAP, has been designed for 3D ligand binding site comparison and similarity searching of a structural proteome.

SMAP can also predict drug side effects and reassign existing drugs to new indications.

However, the computing scale of SMAP is limited.

We have developed a high availability, high performance system that expands the comparison scale of SMAP.

This cloud computing service, called Cloud-PLBS, combines the SMAP and Hadoop frameworks and is deployed on a virtual cloud computing platform.

To handle the vast amount of experimental data on protein-ligand binding site pairs, Cloud-PLBS exploits the MapReduce paradigm as a management and parallelizing tool.

Cloud-PLBS provides a web portal and scalability through which biologists can address a wide range of computer-intensive questions in biology and drug discovery.