. ” Solvent “exposure ” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs

Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/ protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at

DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools

DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key

Real-scale Semantic Web applications, such as Web Portals and E-Marketplaces, require the management of voluminous metadata repositories containing descriptive information (i.e., metadata) about the available Web resources and services. Better knowledge about the meaning, usage, accessibility

Graph has become increasingly important in modelling complicated structures and schemaless data such as proteins, chemical compounds, and XML documents. Given a graph query, it is desirable to retrieve graphs quickly from a large database via graph-based indices. In this paper, we investigate

—particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available inter

Abstract. We present the architecture of an end-to-end semantic search engine that uses a graph data model to enable interactive query answer-ing over structured and interlinked data collected from many disparate sources on the Web. In particular, we study distributed indexing meth-ods for graph

In order to cope with the large amounts of data that have become available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory

of cellular networks as graphs, where nodes represent genes and edges between them represent interactions, either between the encoded proteins or between the encoded proteins and the genes (we use 'genetic interaction' to refer to both types of mechanisms). Available methods fall into four broad