StaRProtein: a web server for prediction of stability of repeat proteins

Repeat proteins have become increasingly important due to their capability to bind to almost any proteins and the potential as alternative therapy to monoclonal antibodies. In the past decade repeat proteins have been designed to mediate specific protein-protein interactions. The tetratricopeptide and ankyrin repeat proteins are two classes of helical repeat proteins that form different binding pockets to accommodate various partners. It is important to understand the factors that define folding and stability of repeat proteins in order to prioritize the most stable designed repeat proteins to further explore their potential binding affinities. Here we developed distance-dependant statistical potentials using two classes of alpha-helical repeat proteins, tetratricopeptide and ankyrin repeat proteins respectively, and evaluated their efficiency in predicting the stability of repeat proteins. We demonstrated that the repeat-specific statistical potentials based on these two classes of repeat proteins showed paramount accuracy compared with non-specific statistical potentials in: 1) discriminate correct vs. incorrect models 2) rank the stability of designed repeat proteins. In particular, the statistical scores correlate closely with the equilibrium unfolding free energies of repeat proteins and therefore would serve as a novel tool in quickly prioritizing the designed repeat proteins with high stability. StaRProtein web server was developed for predicting the stability of repeat proteins.

Methods and Metrics for Fair Server Assessment under Real-Time Financial Workloads

We present a rigorous methodology and new metrics for fair comparison of server and microserver platforms. Deploying our methodology and metrics, we compare a microserver with ARM cores against two servers with ×86 cores running the same real-time financial analytics workload. We define workload-specific but platform-independent performance metrics for platform comparison, targeting both datacenter operators and end users. Our methodology establishes that a server based on the Xeon Phi co-processor delivers the highest performance and energy efficiency. However, by scaling out energy-efficient microservers, we achieve competitive or better energy efficiency than a power-equivalent server with two Sandy Bridge sockets, despite the microserver's slower cores. Using a new iso-QoS metric, we find that the ARM microserver scales enough to meet market throughput demand, that is, a 100% QoS in terms of timely option pricing, with as little as 55% of the energy consumed by the Sandy Bridge server.

Capacity sharing and stealing in dynamic server-based real-time systems

This paper proposes a dynamic scheduler that supports the coexistence of guaranteed and non-guaranteed bandwidth servers to efficiently handle soft-tasks’ overloads by making additional capacity available from two sources: (i) residual capacity allocated but unused when jobs complete in less than their budgeted execution time; (ii) stealing capacity from inactive non-isolated servers used to schedule best-effort jobs. The effectiveness of the proposed approach in reducing the mean tardiness of periodic jobs is demonstrated through extensive simulations. The achieved results become even more significant when tasks’ computation times have a large variance.

Sustentabilidade do SIG municipal da CM de Vila Franca de Xira - Operacionalização de um grupo de trabalho multidisciplinar, estruturalmente suportado pelo ArcGis Server Empertrise Advanced

Relatório de Estágio apresentado para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Gestão do Território.

Rezentralisierung: Server-Based Computing in der Praxis einer Universitätsbibliothek

Der Beitrag beschreibt die Ein- und Durchführung einer Server-basierten Computerinfrastruktur in einer Universitätsbibliothek. Beschrieben wird das so genannte MetaFrame-DV-Konzept der Universitätsbibliothek Kassel, das das dortige Informationsmanagement in den letzten vier Jahren initiiert, konzipiert und umgesetzt hat. Hierbei werden nunmehr nicht mehr nur Applikationsserver z.B. für das CD-Angebot eingesetzt, sondern sämtliche ca. 200 Mitarbeiter- und Funktionsarbeitsplätze über eine Citrix MetaFrame-Installation serverseitig betreut. Besonderes Augenmerk gilt in diesem Beitrag der Konfiguration, der praktischen Administration und den täglichen Arbeitsbedingungen an den Bibliotheksmitarbeiterarbeitsplätzen.

Prediction of global and local model quality in CASP8 using the ModFOLD server

The development of effective methods for predicting the quality of three-dimensional (3D) models is fundamentally important for the success of tertiary structure (TS) prediction strategies. Since CASP7, the Quality Assessment (QA) category has existed to gauge the ability of various model quality assessment programs (MQAPs) at predicting the relative quality of individual 3D models. For the CASP8 experiment, automated predictions were submitted in the QA category using two methods from the ModFOLD server-ModFOLD version 1.1 and ModFOLDclust. ModFOLD version 1.1 is a single-model machine learning based method, which was used for automated predictions of global model quality (QMODE1). ModFOLDclust is a simple clustering based method, which was used for automated predictions of both global and local quality (QMODE2). In addition, manual predictions of model quality were made using ModFOLD version 2.0-an experimental method that combines the scores from ModFOLDclust and ModFOLD v1.1. Predictions from the ModFOLDclust method were the most successful of the three in terms of the global model quality, whilst the ModFOLD v1.1 method was comparable in performance to other single-model based methods. In addition, the ModFOLDclust method performed well at predicting the per-residue, or local, model quality scores. Predictions of the per-residue errors in our own 3D models, selected using the ModFOLD v2.0 method, were also the most accurate compared with those from other methods. All of the MQAPs described are publicly accessible via the ModFOLD server at: http://www.reading.ac.uk/bioinf/ModFOLD/. The methods are also freely available to download from: http://www.reading.ac.uk/bioinf/downloads/.

The ModFOLD server for the quality assessment of protein structural models

The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment.

The DISOPRED server for the prediction of protein disorder

Dynamically disordered regions appear to be relatively abundant in eukaryotic proteomes. The DISOPRED server allows users to submit a protein sequence, and returns a probability estimate of each residue in the sequence being disordered. The results are sent in both plain text and graphical formats, and the server can also supply predictions of secondary structure to provide further structural information.