Structural protein interactions: From months to minutes [chapter]

P. Dafas, J. Gomoluch, A. Kozlenkov, M. Schroeder
2004 Advances in Parallel Computing  
Protein interactions are important to understand the function of proteins. PSIMAP is a protein interaction map derived from protein structures in the Protein Databank PDB and the Structural Classification of Proteins SCOP. In this paper we review how to reduce the computation of PSIMAP from months to minutes, first by designing a new effective algorithm and second by distributing the computation over a Linux PC farm using a simple scheduling mechanism. From this experience we derive some
more » ... conclusions: Besides computational complexity, most problems in bioinformatics require information integration and this integration is semantically complex. We sketch our relevant work to tackle computational and semantic complexity. Regarding the former, we classify problems and infrastructure and review how market-based load-balancing can be applied. Regarding the latter, we outline a Java-based rule-engine, which allows users to declaratively specify workflows separate from implementation details.
doi:10.1016/s0927-5452(04)80084-4 fatcat:2jprrk3z2jgcvf7rdyakzsnecu