Search results for "INFORMATICS"
showing 10 items of 2542 documents
The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis
2021
Abstract Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either mi…
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
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
2018
Abstract Motivation K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability. Results We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays—one for k-mer representation and the other for frequency encoding. Exper…
Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs
2016
Abstract One of use cases for metabolic network optimisation of biotechnologically applied microorganisms is the in silico design of new strains with an improved distribution of metabolic fluxes. Global stochastic optimisation methods (genetic algorithms, evolutionary programing, particle swarm and others) can optimise complicated nonlinear kinetic models and are friendly for unexperienced user: they can return optimisation results with default method settings (population size, number of generations and others) and without adaptation of the model. Drawbacks of these methods (stochastic behaviour, undefined duration of optimisation, possible stagnation and no guaranty of reaching optima) cau…
DFT studies of COOH tip-functionalized zigzag and armchair single wall carbon nanotubes
2011
Structure and energy calculations of pristine and COOH-modified model single wall carbon nanotubes (SWCNTs) of different length were performed at B3LYP/6-31G* level of theory. From 1 to 9 COOH groups were added at the end of the nanotube. The differences in structure and energetics of partially and fully functionalized SWCNTs at one end of the nanotube are observed. Up to nine COOH groups could be added at one end of (9,0) zigzag SWCNT in case of full functionalization. However, for (5,5) armchair SWCNT, the full functionalization was impossible due to steric crowding and rim deformation. The dependence of substituent attachment energy on the number of substituents at the carbon nanotube ri…
Crystal structure of ethyl 2-(di-eth-oxy-phosphor-yl)-2-(2,3,4-tri-meth-oxy-phen-yl)acetate.
2014
The title compound, C17H27O8P, was prepared by Michaelis–Arbuzov reaction of ethyl 2-bromo-2-(2,3,4-trimethoxyphenyl)acetate and triethyl phosphite. Such compounds rarely crystallize, but single crystals were recovered after the initial oil was left for approximately 10 years. The bond angle of thesp3-hybridized C atom connecting the benzene derivative with the phospho unit is widened marginally [112.5 (2)°]. The terminal P—O bond length of 1.464 (2) Å clearly indicates a double bond, whereas the two O atoms of the ethoxy groups connected to the phosphorous atom have bond lengths of 1.580 (2) Å and 1.581 (3) Å. The three methoxy groups emerge out of the benzene-ring plane due to steric hind…
Mobile Mental Wellness Training for Stress Management: Feasibility and Design Implications Based on a One-Month Field Study
2013
Background: Prevention and management of work-related stress and related mental problems is a great challenge. Mobile applications are a promising way to integrate prevention strategies into the everyday lives of citizens. Objective: The objectives of this study was to study the usage, acceptance, and usefulness of a mobile mental wellness training application among working-age individuals, and to derive preliminary design implications for mobile apps for stress management. Methods: Oiva, a mobile app based on acceptance and commitment therapy (ACT), was designed to support active learning of skills related to mental wellness through brief ACT-based exercises in the daily life. A one-month …
Determinant Factors of Public Acceptance of Stress Management Apps: Survey Study
2019
BackgroundChronic stress is a major public health concern. Mobile health (mHealth) apps can help promote coping skills in daily life and prevent stress-related issues. However, little is known about the determinant factors of public acceptance of stress management in relation to preferences for psychological services.ObjectiveThe aim of this survey study was to (1) assess determinant factors of public acceptance (behavioral use intention) of stress management apps based on an adapted and extended version of the Unified Theory of Acceptance and Use of Technology (UTAUT) model and (2) explore preferences for mHealth apps compared with other mental health services.MethodsUsing convenience samp…
Prediction of perception using structure–activity models
2016
IntroductionThe possible link between the molecular structure and a biological activity was pointed out by Linus Pauling (1946) just before the middle of the 20th century. Nevertheless, this concept has been already suggested a century before by Emil Fisher and “lock-and-key” theory: “To use a metaphor, I would say that enzyme and glucoside are such lock and key that fit together in order to exert a reciprocal chemical effect on each other”a (Fischer, 1894). The notion that the biological properties of a compound would be a function of its chemical characteristics is now well admitted, and is closely linked to that of pharmacophore. The pharmacophore concept is related to the interaction of…
Complex Detection in Protein-Protein Interaction Networks: A Compact Overview for Researchers and Practitioners
2012
The availability of large volumes of protein-protein interaction data has allowed the study of biological networks to unveil the complex structure and organization in the cell. It has been recognized by biologists that proteins interacting with each other often participate in the same biological processes, and that protein modules may be often associated with specific biological functions. Thus the detection of protein complexes is an important research problem in systems biology. In this review, recent graph-based approaches to clustering protein interaction networks are described and classified with respect to common peculiarities. The goal is that of providing a useful guide and referenc…