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We describe predictions of the structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target domains without detectable sequence similarity to a protein of known structure and to build long loop insertions (and N-and C-terminal extensions) in cases where a structural template was available.(More)
Plasma Posters are large screen, digital, interactive poster-boards situated in public spaces, designed to facilitate informal content sharing within teams, groups, organizations and communities. While interest i interactive community poster boards has grown recently, few successful examples have been reported. In this paper we describe an ongoing(More)
Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. It combines template-based and de novo structure prediction methods in an attempt to produce high quality models that cover every residue of a submitted sequence. The first step in the procedure is the automatic detection of the locations of(More)
Macromolecular modeling and design are increasingly useful in basic research, biotechnology, and teaching. However, the absence of a user-friendly modeling framework that provides access to a wide range of modeling capabilities is hampering the wider adoption of computational methods by non-experts. RosettaScripts is an XML-like language for specifying(More)
Although de novo computational enzyme design has been shown to be feasible, the field is still in its infancy: the kinetic parameters of designed enzymes are still orders of magnitude lower than those of naturally occurring ones. Nonetheless, designed enzymes can be improved by directed evolution, as recently exemplified for the designed Kemp eliminase(More)
Although there exists a multitude of diierent inspection processes, the basic process has remained unchanged since it was rst deened by Fagan in 1976. This process has as its central component an inspection meeting which all participants attend. But is this meeting cost eeective? Recent empirical work has indicated this is not the case. An inspection model(More)
In this paper, we describe the YeTi information sharing system that has been designed to foster community building through informal digital content sharing. The YeTi system is a general information parsing, hosting and distribution infrastructure, with interfaces designed for individual and public content reading. In this paper we describe the YeTi public(More)
We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high-resolution search in which all(More)
The sharing of digital materials within online communities has increased significantly in recent years. Our work focuses on promoting community information sharing in public spaces using large screen, interactive, digital poster boards called the Plasma Posters. In this chapter we first describe our fieldwork-led, iterative design process, and elaborate a(More)