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Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several(More)
A correlation analysis of the amino acid composition and the cellular location of a protein is presented. The statistical analysis discriminates among the following five protein classes: integral membrane proteins, anchored membrane proteins, extracellular proteins, intracellular proteins and nuclear proteins. This segregation into protein classes related(More)
Protein-protein interactions are central to most biological processes. Although much recent effort has been put into methods to identify interacting partners, there has been a limited focus on how these interactions compare with those known from three-dimensional (3D) structures. Because comparison of protein interactions often involves considering(More)
Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions, bioinformatics, and electron microscopy. Here we use interactions of known three-dimensional structure to model a large set of yeast complexes, which we also screen(More)
SUMMARY InterPreTS (Interaction Prediction through Tertiary Structure) is a web-based version of our method for predicting protein-protein interactions (Aloy and Russell, 2002, PROC: Natl Acad. Sci. USA, 99, 5896-5901). Given a pair of query sequences, we first search for homologues in a database of interacting domains (DBID) of known three-dimensional(More)
The database of 3D Interacting Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur. It also offers an overview of how similar in structure are(More)
Previous studies have suggested that nature is restricted to about 1,000 protein folds to perform a great diversity of functions. Here, we use protein interaction data from different sources and three-dimensional structures to suggest that the total number of interaction types is also limited, and estimate that most interactions in nature will conform to(More)
Network-centered approaches are increasingly used to understand the fundamentals of biology. However, the molecular details contained in the interaction networks, often necessary to understand cellular processes, are very limited, and the experimental difficulties surrounding the determination of protein complex structures make computational modeling(More)
A major problem in genome annotation is whether it is valid to transfer the function from a characterised protein to a homologue of unknown activity. Here, we show that one can employ a strategy that uses a structure-based prediction of protein functional sites to assess the reliability of functional inheritance. We have automated and benchmarked a method(More)
Network and systems biology offer a novel way of approaching drug discovery by developing models that consider the global physiological environment of protein targets, and the effects of modifying them, without losing the key molecular details. Here we review some recent advances in network and systems biology applied to human health, and discuss how they(More)