title: Cloud computing for protein-ligand binding site comparison.
abstract: 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.
authors.affiliation: Department of Computer Science and Communication Engineering, Providence University, Taiwan Boulevard, Shalu District, Taichung 43301, Taiwan. clhung@pu.edu.tw
authors.forename: Che-Lun
authors.initials: CL
authors.lastname: Hung
authors.forename: Guan-Jie
authors.initials: GJ
authors.lastname: Hua
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D008024:Ligands; D011506:Proteins / Q000378:metabolism*; D012984:Software; D013997:Time Factors
chemical_list: D008024:Ligands; D011506:Proteins