34,413 research outputs found
Jeeva: Enterprise Grid-enabled Web Portal for Protein Secondary Structure Prediction
This paper presents a Grid portal for protein secondary structure prediction
developed by using services of Aneka, a .NET-based enterprise Grid technology.
The portal is used by research scientists to discover new prediction structures
in a parallel manner. An SVM (Support Vector Machine)-based prediction
algorithm is used with 64 sample protein sequences as a case study to
demonstrate the potential of enterprise Grids.Comment: 7 page
Incorporating prediction models in the SelfLet framework: a plugin approach
A complex pervasive system is typically composed of many cooperating
\emph{nodes}, running on machines with different capabilities, and pervasively
distributed across the environment. These systems pose several new challenges
such as the need for the nodes to manage autonomously and dynamically in order
to adapt to changes detected in the environment. To address the above issue, a
number of autonomic frameworks has been proposed. These usually offer either
predefined self-management policies or programmatic mechanisms for creating new
policies at design time. From a more theoretical perspective, some works
propose the adoption of prediction models as a way to anticipate the evolution
of the system and to make timely decisions. In this context, our aim is to
experiment with the integration of prediction models within a specific
autonomic framework in order to assess the feasibility of such integration in a
setting where the characteristics of dynamicity, decentralization, and
cooperation among nodes are important. We extend an existing infrastructure
called \emph{SelfLets} in order to make it ready to host various prediction
models that can be dynamically plugged and unplugged in the various component
nodes, thus enabling a wide range of predictions to be performed. Also, we show
in a simple example how the system works when adopting a specific prediction
model from the literature
The Phyre2 web portal for protein modeling, prediction and analysis
Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission
- …