Search results for "Web server"
showing 10 items of 45 documents
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
Mutational Characterization of the Bile Acid Receptor TGR5 in Primary Sclerosing Cholangitis
2010
Background: TGR5, the G protein-coupled bile acid receptor 1 (GPBAR1), has been linked to inflammatory pathways as well as bile homeostasis, and could therefore be involved in primary sclerosing cholangitis (PSC) a chronic inflammatory bile duct disease. We aimed to extensively investigate TGR5 sequence variation in PSC, as well as functionally characterize detected variants.Methodology/Principal Findings: Complete resequencing of TGR5 was performed in 267 PSC patients and 274 healthy controls. Six nonsynonymous mutations were identified in addition to 16 other novel single-nucleotide polymorphisms. To investigate the impact from the nonsynonymous variants on TGR5, we created a receptor mod…
Sensitivity Analysis Of Key Customers And Revenue-Oriented Admission Control And Scheduling Algorithm
2013
Received: 15 January 2013 Abstract Accepted: 2 February 2013 The paper deals with the problem of Quality of Web Service (QoWS) in e-commerce Web servers, i.e. in retail Web stores. It concerns the admission control and scheduling algorithm for a Web server system, which aims at preventing the system from overload to provide high QoWS level and ultimately, to increase Web site’s conversion rate, i.e. to turn more visitors into customers. The sensitivity of the algorithm to changes in its basic parameter values was analyzed by using a simulation-based approach. Special attention was paid to evaluation of the parameter impact on conventional and business-related system performance metrics.
Proposal of a neuro-fuzzy model of a WWW server
2005
This paper presents the ways of designing simulation models of Web servers. At the beginning queuing network models are introduced, those models are generally known and often used in the initial phase of research on particular technical solutions. Next, an entirely new approach to the issue discussed is presented - neuro-fuzzy models, thanks to which, it is possible to automate the process of designing simulation models. The results of comparative tests of these two models are presented. Based on these results it can be concluded that neuro-fuzzy models are accurate and can be used in simulation research.
REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences
2020
Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses f…
Growing Hierarchical Self-organizing Maps and Statistical Distribution Models for Online Detection of Web Attacks
2013
In modern networks, HTTP clients communicate with web servers using request messages. By manipulating these messages attackers can collect confidential information from servers or even corrupt them. In this study, the approach based on anomaly detection is considered to find such attacks. For HTTP queries, feature matrices are obtained by applying an n-gram model, and, by learning on the basis of these matrices, growing hierarchical self-organizing maps are constructed. For HTTP headers, we employ statistical distribution models based on the lengths of header values and relative frequency of symbols. New requests received by the web-server are classified by using the maps and models obtaine…
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins
2020
Abstract Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToL…
SKINK: a web server for string kernel based kink prediction in α-helices
2014
Abstract Motivation: The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. Here, we present a new web server, called SKINK, for string kernel based kink prediction. Extending our previous study, we also annotate the most probable kink position in a given α-helix sequence. Availability and implementation: The SKINK web server is freely accessible at http://biows-inf.zdv.uni-mainz.de/skink. Moreover, SKINK is a module of the BALL software, also freely available at www.ballview.org. Contact: benny.kneissl@roche.com
LipiDisease: associate lipids to diseases using literature mining
2021
Abstract Summary Lipids exhibit an essential role in cellular assembly and signaling. Dysregulation of these functions has been linked with many complications including obesity, diabetes, metabolic disorders, cancer and more. Investigating lipid profiles in such conditions can provide insights into cellular functions and possible interventions. Hence the field of lipidomics is expanding in recent years. Even though the role of individual lipids in diseases has been investigated, there is no resource to perform disease enrichment analysis considering the cumulative association of a lipid set. To address this, we have implemented the LipiDisease web server. The tool analyzes millions of recor…
Bot recognition in a Web store: An approach based on unsupervised learning
2020
Abstract Web traffic on e-business sites is increasingly dominated by artificial agents (Web bots) which pose a threat to the website security, privacy, and performance. To develop efficient bot detection methods and discover reliable e-customer behavioural patterns, the accurate separation of traffic generated by legitimate users and Web bots is necessary. This paper proposes a machine learning solution to the problem of bot and human session classification, with a specific application to e-commerce. The approach studied in this work explores the use of unsupervised learning (k-means and Graded Possibilistic c-Means), followed by supervised labelling of clusters, a generative learning stra…