Structural biology is based on an important observation: the function of a biomolecule is determined by its three-dimensional structure and its physico-chemical properties. Hence, visualization, ...modeling, and simulation of molecular structures and of their properties are crucial tools of the field. Typically, the graphical interfaces to molecular modeling packages are aimed at domain experts with significant experience and require an extensive learning period. But in many scenarios, such as teaching, presentations, and demonstrations, it would be highly preferable to have an intuitive environment for showcasing molecular functionality. Ideally, it should support simple preparation of the presentations as well as their convenient display. To keep the user interface simple and focused, the environment should be particularly adapted to the processing of molecular structures. Here, we present such a presentation framework, called PresentaBALL, which uses established web technology standards to provide a freely configurable browser-based interface into the extensive modeling and visualization capabilities of the Biochemical Algorithms Library (BALL). The web interface is embedded into BALL's graphical frontend BALLView, and provides complete, interactive access to the loaded molecular data. PresentaBALL enables researchers in biology with basic knowledge in HTML, JavaScript, or Python to easily setup academic tutorials, demonstrations, or scientific presentations and lectures with 3D structure content and interactive workflows. Owing to its flexible design, other modern forms of teaching and presentation, such as massive open online courses (MOOC) can also use PresentaBALL as their core component. PresentaBALL is licensed under the GNU Public License (GPL) and will be made available in BALL/BALLView, starting with the upcoming release (1.5).
Lectin–sugar interaction Neumann, Dirk; Kohlbacher, Oliver; Lenhof, Hans‐Peter ...
European journal of biochemistry,
March 2002, Volume:
269, Issue:
5
Journal Article
Peer reviewed
Although a steadily increasing number of protein–ligand docking experiments have been performed successfully, there are only few studies concerning protein–sugar interactions. In this study, we ...investigate the interaction of wheat germ agglutinin (WGA) with N‐acetylglucosamine and a number of its derivatives and predict the binding free energies using flexible docking techniques. To assess the quality of our predictions, we also determined those binding free energies experimentally in cell‐binding studies. The predicted binding site, ligand orientation, and details of the binding mode are in perfect agreement with the known crystal structure of WGA with a sialoglycopeptide. Furthermore, we obtained an excellent linear correlation of our predicted binding free energies with both our own data and experimental data from the literature Monsigny, M., Roche, A.C., Sene, C., Maget Dana, R. & Delmotte, F. (1980) Eur. J. Biochem.104, 147–153.. In both cases, predicted energies were within 1.0 kJ·mol−1 of the experimental value. These results illustrate the usefulness of docking‐based methods for the qualitative and quantitative prediction of protein–carbohydrate interactions. The insights gained from such theoretical studies may be used to complement the results from the still scarce crystal structures.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
q-gram based database searching using a suffix array (QUASAR) Burkhardt, Stefan; Crauser, Andreas; Ferragina, Paolo ...
Annual Conference on Research in Computational Molecular Biology: Proceedings of the third annual international conference on Computational molecular biology; 11-14 Apr. 1999,
04/1999
Conference Proceeding
Measuring properties of molecular surfaces using ray casting Phillips, Mike; Georgiev, Iliyan; Dehof, Anna Katharina ...
2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW),
2010-April
Conference Proceeding
Open access
Molecular geometric properties, such as volume, exposed surface area, and occurrence of internal cavities, are important inputs to many applications in molecular modeling. In this work we describe a ...very general and highly efficient approach for the accurate computation of such properties, which is applicable to arbitrary molecular surface models. The technique relies on a high performance ray casting framework that can be easily adapted to the computation of further quantities of interest at interactive speed, even for huge models.
Let
S be a set of
n points in
d-space, where
d ≥ 2 is a constant, and let 1 ≤
k ≤
n be an integer. A unified approach is given for solving the problem of finding a subset of
S of size
k that ...minimizes some closeness measure, such as the diameter, perimeter or the circumradius. Moreover, data structures are given that maintain such a subset under insertions and deletions of points.
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BN++ – A Biological Information System Küntzer, Jan; Blum, Torsten; Gerasch, Andreas ...
Journal of integrative bioinformatics,
12/2006, Volume:
3, Issue:
2
Journal Article
Peer reviewed
Open access
Recent years have seen an explosive growth in the amount of biochemical data available. Numerous databases have been established and are being used as an essential resource by biologists around the ...world. The sheer amount and heterogeneity of these data poses a major challenge: data integration and, based thereupon, the integrative analysis of these data. We present BN++, the biochemical network library, a powerful software package for integrating, analyzing, and visualizing biochemical data in the context of networks. BN++ is based on a comprehensive and extensible object model (BioCore), which has been implemented as a C++ framework, a Java class library, and a relational database. The C++ framework is used to efficiently import, integrate, and analyze the data, which is stored in a data warehouse. The Java-based viewer (BiNA) provides a powerful platform-independent visualization of the data using sophisticated graph layout algorithms. Currently, the data warehouse imports and integrates data from about a dozen important databases including, among others, sequence data, metabolic and regulatory networks, and protein interaction data. We illustrate the usefulness of BN++ with a few select example applications.
Availability: BN++ is open source software available from our website at www.bnplusplus.org.
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