3D Library Research Articles

Combining ethnopharmacology and virtual screening for lead structure discovery: COX-inhibitors as application example.

Virtual screening of large libraries of organic compounds combined with pharmacological high throughput screening is widely used for drug discovery in the pharmaceutical industry. Our aim was to explore the efficiency of using a biased 3D database comprising secondary metabolites from antiinflammatory medicinal plants as a source for the virtual screening. For this study pharmacophore models of cyclooxygenase I and II (COX-1, COX-2), key enzymes in the inflammation process, were generated with structure-based as well as common feature based modeling, resulting in three COX hypotheses. Four different multiconfomational 3D databases limited in molecular weight between 300 and 700 Da were applied to the screening in order to compare and analyze the obtained hit rates. Two of them were created in-house (DIOS, NPD). The database DIOS consists of 2752 compounds from phytochemical reports of antiinflammatory medicinal plants described by the ethnopharmacological source 'De material medica' of Pedanius Dioscorides, whereas NPD contains almost 80,000 compounds gathered arbitrarily from natural sources. In addition, two available multiconformational 3D libraries comprising marketed and development drug substances (DWI and NCI), mainly originating from synthesis, were used for comparison. As a test of the pharmacophore models' capability in natural sources, the models were used to search for known COX inhibitory natural products. This was achieved with some exceptions, which are discussed in the paper. Depending on the hypothesis used, DWI and NCI library searches produced hit rates in the range of 6.6% to 13.7%. A slight increase of the number of molecules assessed for binding was achieved with the database of natural products (NPD). Using the biased 3D database DIOS, however, the average increase of efficiency reached 77% to 133% compared to the hit rates resulting from WDI and NCI. The statistical benefit of a combination of an ethnopharmacological approach with the potential of computer aided drug discovery by in silico screening was demonstrated exemplified on the applied targets COX-1 and COX-2.

Multiphysics Modelling Environment for Continuum And Discrete Dynamics

A model-development environment for simulation of discrete and continuum dynamics in complex 3D geometries is described. This environment is based on 3D libraries for manipulation of geometrical primitives, object-oriented multidomain modelling paradigm, continuum solvers on unstructured meshes, discrete particle solvers, and a tool-assisted grid generation technique. The numerical approach is based on combined control-volume and finite-element methods of continuum mechanics and Lagrangian particle dynamics method. Several prototype example cases of complex continuum mechanical systems are considered, such as flow in bifurcating channels, including particle transport and deposition, flow interactions with flexible membranes and rigid structures, and a simplified model of molecular dynamics represented by a system of particles and bonds.

Multiphysics Modelling Environment for Continuum and Discrete Dynamics

AbstractA model-development environment for simulation of discrete and continuum dynamics in complex 3D geometries is described. This environment is based on 3D libraries for manipulation of geometrical primitives, object-oriented multidomain modelling paradigm, continuum solvers on unstructured meshes, discrete particle solvers, and a tool-assisted grid generation technique. The numerical approach is based on combined control-volume and finite-element methods of continuum mechanics and Lagrangian particle dynamics method. Several prototype example cases of complex continuum mechanical systems are considered, such as flow in bifurcating channels, including particle transport and deposition, flow interactions with flexible membranes and rigid structures, and a simplified model of molecular dynamics represented by a system of particles and bonds.

3D motion retrieval with motion index tree

With the development of Motion capture techniques, more and more 3D motion libraries become available. In this paper, we present a novel content-based 3D motion retrieval algorithm. We partition the motion library and construct a motion index tree based on a hierarchical motion description. The motion index tree serves as a classifier to determine the sub-library that contains the promising similar motions to the query sample. The Nearest Neighbor rule-based dynamic clustering algorithm is adopted to partition the library and construct the motion index tree. The similarity between the sample and the motion in the sub-library is calculated through elastic match. To improve the efficiency of the similarity calculation, an adaptive clustering-based key-frame extraction algorithm is adopted. The experiment demonstrates the effectiveness of this algorithm.

Integrated Internet collaboration

The last four years have brought tremendous advances in software applications, software tools, and software systems for modernizing, consolidating, and coordinating an enterprise's computer applications. Many companies have existing legacy applications and databases and want to continue to use them while adding or migrating to a new set of applications that exploit the Internet, e-commerce, Intranet, remote collaboration, independence from operating systems, and other new technologies. They should be able to do this because the new software tools have orders of magnitude more functionality than mid-1990s software applications that relied on Xwindows, some mathematical libraries, and a compiler. The built-in network communications, remote collaboration support, database support, and 3D and 2D graphic libraries give programmers the power to create industrial strength solutions that integrate all these new technologies in a specific application—for example, a data-processing or depth-imaging system.

Virtual heritage: what next?

Virtual heritage is the use of computer-based interactive technologies to record, preserve or recreate artifacts, sites and actors of historic, artistic, religious and cultural significance and to deliver the results openly to a global audience in such a way as to provide formative educational experiences through electronic manipulations of time and space. Where do we go from here, and what can we expect in the next decade? Already we're witnessing the evolution of systems making virtual reality (VR) accessible to social and working groups for applications hitherto considered out of the question. For those with just a basic PC and access to the Web, VR is now a technology that promotes active participation, through contributions to virtual libraries or repositories, or becoming involved as avatars (virtual humans) in shared electronic communities. We can now harness the power of video games engines, backed up with tutorials, patches and 3D model libraries from the Web. VR is no longer a limited sensory experience, accessible to a few fortunate individuals. Neither is it a technology destined to replace the real experience of traveling to a historical site or museum and experiencing the true ambience and splendor of the past first-hand. It's a means by which we can increase our understanding of (and respect for) our sociological, cultural and natural past, with the ultimate aim of making our future a more rewarding experience for those yet to come.

3D visualization library for multimodal medical images

This study focuses on three-dimensional (3D) presentations of medical images such as magnetic resonance (MR) images and computed tomography (CT) images. Also multimodal presentations of medical images and signals, including different visualization techniques are considered. A C++ class library together with graphical user interfaces was developed for presenting the results. The implemented software operates in PC/Windows™ environment. It was tested with various medical images including raw MR and CT data and segmented images, and was applied in a hospital environment. The software operates relatively fast and the quality of resulting pictures is adequate for all tested medical applications. Further applications of 3D presentations in clinical medicine are considered.

Obliq-3D: a high-level, fast-turnaround 3D animation system

Describes Obliq-3D, a high-level, fast-turnaround system for building 3D animations. Obliq-3D consists of an interpreted language that is embedded into a 3D animation library. This library is based on a few simple, yet powerful constructs that allow programmers to describe 3D scenes and animations of such scenes. By virtue of its interpretive nature, Obliq-3D provides a fast-turnaround environment. The combination of simplicity and fast turnaround allows programmers to construct nontrivial animations quickly and easily. The paper is divided into three major parts. The first part introduces the basic concepts of Obliq-3D, using a series of graduated examples. The second part shows how the system can be used to implement cone trees. The third part develops a complete animation of Dijkstra's (1959) shortest-path algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>