Three Dimensional Protein Structure Comparison Web Services on the MapReduce Framework

Protein structures are essential for correct biological functions because similar structures between proteins allow molecular recognition. Identifying similar structures between proteins provide the opportunity to recognize homology that is undetectable by sequence comparison. Thus comparison and alignment of protein structures represents a powerful means of discovering functions, yielding direct insight into the molecular mechanisms. Currently, there are several techniques available in attempting to find the optimal alignment of shared structural motifs between two proteins. This paper adopts approach using the MapReduce paradigm to parallelize tools and manage their execution. The experiment shows that the map/reduce-paralleled from the original sequential combinatorial algorithm performs well on the real-world data obtained in from the PDB data set; the computation efficiency can be effectively improved proportional to the number of processors being used.