7,572 research outputs found
The TriForC database : a comprehensive up-to-date resource of plant triterpene biosynthesis
Triterpenes constitute a large and important class of plant natural products with diverse structures and functions. Their biological roles range from membrane structural components over plant hormones to specialized plant defence compounds. Furthermore, triterpenes have great potential for a variety of commercial applications such as vaccine adjuvants, anti-cancer drugs, food supplements and agronomic agents. Their biosynthesis is carried out through complicated, branched pathways bymultiple enzyme types that include oxidosqualene cyclases, cytochrome P450s, and UDP-glycosyltransferases. Given that the number of characterized triterpene biosynthesis enzymes has been growing fast recently, the need for a database specifically focusing on triterpene enzymology became eminent. Here, we present the TriForC database (http://bioinformatics. psb. ugent. be/triforc/), encompassing a comprehensive catalogue of triterpene biosynthesis enzymes. This highly interlinked database serves as a user-friendly access point to versatile data sets of enzyme and compound features, enabling the scanning of a complete catalogue of experimentally validated triterpene enzymes, their substrates and products, as well as the pathways they constitute in various plant species. The database can be accessed by direct browsing or through convenient search tools including keyword, BLAST, plant species and substructure options. This database will facilitate gene mining and creating genetic toolboxes for triterpene synthetic biology
TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data
Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, and easy-to-share pipelines. While documentation for such tools is available, there are only a few freely accessible examples that teach the underlying concepts focused on CADD, especially addressing users new to the field. Here, we present TeachOpenCADD, a teaching platform developed by students for students, using open source compound and protein data as well as basic and CADD-related Python packages. We provide interactive Jupyter notebooks for central CADD topics, integrating theoretical background and practical code. TeachOpenCADD is freely available on GitHub: https://github.com/volkamerlab/TeachOpenCAD
Open-ended evolution to discover analogue circuits for beyond conventional applications
This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10710-012-9163-8. Copyright @ Springer 2012.Analogue circuits synthesised by means of open-ended evolutionary algorithms often have unconventional designs. However, these circuits are typically highly compact, and the general nature of the evolutionary search methodology allows such designs to be used in many applications. Previous work on the evolutionary design of analogue circuits has focused on circuits that lie well within analogue application domain. In contrast, our paper considers the evolution of analogue circuits that are usually synthesised in digital logic. We have developed four computational circuits, two voltage distributor circuits and a time interval metre circuit. The approach, despite its simplicity, succeeds over the design tasks owing to the employment of substructure reuse and incremental evolution. Our findings expand the range of applications that are considered suitable for evolutionary electronics
The MultiDark Database: Release of the Bolshoi and MultiDark Cosmological Simulations
We present the online MultiDark Database -- a Virtual Observatory-oriented,
relational database for hosting various cosmological simulations. The data is
accessible via an SQL (Structured Query Language) query interface, which also
allows users to directly pose scientific questions, as shown in a number of
examples in this paper. Further examples for the usage of the database are
given in its extensive online documentation (www.multidark.org). The database
is based on the same technology as the Millennium Database, a fact that will
greatly facilitate the usage of both suites of cosmological simulations. The
first release of the MultiDark Database hosts two 8.6 billion particle
cosmological N-body simulations: the Bolshoi (250/h Mpc simulation box, 1/h kpc
resolution) and MultiDark Run1 simulation (MDR1, or BigBolshoi, 1000/h Mpc
simulation box, 7/h kpc resolution). The extraction methods for halos/subhalos
from the raw simulation data, and how this data is structured in the database
are explained in this paper. With the first data release, users get full access
to halo/subhalo catalogs, various profiles of the halos at redshifts z=0-15,
and raw dark matter data for one time-step of the Bolshoi and four time-steps
of the MultiDark simulation. Later releases will also include galaxy mock
catalogs and additional merging trees for both simulations as well as new large
volume simulations with high resolution. This project is further proof of the
viability to store and present complex data using relational database
technology. We encourage other simulators to publish their results in a similar
manner.Comment: 28 pages, 9 figures, submitted to New Astronom
NASTRAN interfacing modules within the Integrated Analysis Capability (IAC) Program
The IAC program provides the framework required for the development of an extensive multidisciplinary analysis capability. Several NASTRAN related capabilities were developed which can all be expanded in a routine manner to meet in-house unique needs. Plans are to complete the work discussed herein and to provide it to the engineering community through COSMIC. Release is to be after the current IAC Level 2 contract work on the IAC executive system is completed and meshed with the interfacing modules and analysis capabilities under development at the GSFC
Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis
This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work
Resource Letter: Gravitational Lensing
This Resource Letter provides a guide to a selection of the literature on
gravitational lensing and its applications. Journal articles, books, popular
articles, and websites are cited for the following topics: foundations of
gravitational lensing, foundations of cosmology, history of gravitational
lensing, strong lensing, weak lensing, and microlensing.Comment: Resource Letter, 2012, in press
(http://ajp.dickinson.edu/Readers/resLetters.html); 21 pages, no figures;
diigo version available at
http://groups.diigo.com/group/gravitational-lensin
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