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Confab - Systematic generation of diverse low-energy conformers
Noel M O'Boyle, Tim Vandermeersch, Christopher J Flynn, Anita R Maguire, Geoffrey R Hutchison
Journal of Cheminformatics , 2011, DOI: 10.1186/1758-2946-3-8
Abstract: Confab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 ? at a diversity level of 1.5 ? and an energy cutoff of 50 kcal/mol.Confab is available from http://confab.googlecode.com webcite.The generation of molecular conformations is an essential part of many computational analyses in chemistry, particularly in the field of computational drug design. Methods such as 3D QSAR, protein-ligand docking and pharmacophore generation and searching [1] all require the generation of conformers, whether on-the-fly (as part of the method) or pre-generated by a stand-alone conformer generator. In contrast to 3D structure generators (such as CORINA [2], DG-AMMOS [3] and smi23d [4]), which focus on the generation of a single low-energy conformation, conformation generators create an ensemble of conformers that cover the entire space of low-energy conformations or that part of conformational space occupied by biologically-relevant conformers.Several proprietary conformation generators are currently available (including OMEGA [5], ROTATE [6], Catalyst [7], Confort [8], ConfGen [9], Balloon [10] and MED-3DMC [11] among others) but only recently have open source conformation generators appeared: Frog2 [12] generates conformers using a Monte Carlo approach, while Multiconf-DOCK [13] adapts the systematic search code from DOCK5 [14] to generate diverse conformers via a torsion-driving approach.Confab 1.0 is the first release of Confab, an open source conformation generator whose goal is the systematic coverage of c
Open Babel: An open chemical toolbox
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison
Journal of Cheminformatics , 2011, DOI: 10.1186/1758-2946-3-33
Abstract: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org webcite.The history of chemical informatics has included a huge variety of textual and computer representations of molecular data. Such representations focus on specific atomic or molecular information and may not attempt to store all possible chemical data. For example, line notations like Daylight SMILES [1] do not offer coordinate information, while crystallographic or quantum mechanical formats frequently do not store chemical bonding data. Hydrogen atoms are frequently omitted from x-ray crystallography due to the difficulty in establishing coordinates, and are often ignored by some file formats as the "implicit valence" of heavy atoms that indicates their presence. Other types of representations require specification of atom types on the basis of a specific valence bond model, inclusion of c
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
Hanwell Marcus D,Curtis Donald E,Lonie David C,Vandermeersch Tim
Journal of Cheminformatics , 2012, DOI: 10.1186/1758-2946-4-17
Abstract: Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.
La fouille de Qafzeh
Bernard Vandermeersch
Bulletin du Centre de Recherche Fran?ais de Jérusalem , 2008,
Abstract: La fouille de la grotte de Qafzeh par René Neuville, alors en poste au Consulat général de France à Jérusalem, a débuté réellement en 1934, après qu’un sondage, réalisé l’année précédente, eut révélé toute l’importance de ce gisement. Il faut, en effet savoir, pour ceux qui connaissent le site dans son état actuel, que lorsque R. Neuville a commencé ses recherches, les sédiments et les figuiers de barbarie masquaient presque complètement l’entrée de la grotte dans laquelle on ne pouvait pénét...
Qafzeh, histoire des découvertes
Bernard Vandermeersch
Bulletin du Centre de Recherche Fran?ais de Jérusalem , 2009,
Abstract: Le Mont Qafzeh ou Mont du Précipice (Har Kedumin en hébreu, Jabal al-Qafza en arabe) culmine à 392 m, à environ 2,5 km au sud de la ville ancienne de Nazareth. La grotte qui porte son nom s’ouvre dans son flanc sud-ouest à 220 m d’altitude et à 7 m au-dessus du talweg du Wadi el Hadj ou Wadi du Pèlerin. Ce wadi est un petit torrent intermittent né au pied de la ville et qui aboutit à la plaine d’Esdrelon. La grotte s’ouvre à environ 200 m de son débouché sur la plaine. Jusqu’à récemment on y ...
The excavation of Qafzeh
Bernard Vandermeersch
Bulletin du Centre de Recherche Fran?ais de Jérusalem , 2008,
Abstract: The excavation of the Qafzeh cave by René Neuville, while he was serving as the French Consul General in Jerusalem, began in earnest in 1934, after a test excavation conducted the year before revealed the extent of the importance of this site. For those who are familiar with Qafzeh as it stands now, it should be pointed out that when R. Neuville began his studies, sediment and Barbary figs almost completely concealed the entrance to the cave, which could not be entered standing up. The cave o...
A Study on Configuration and Integration of Sub-Systems to System-of-Systems with Rule Verification  [PDF]
Tim Warnecke
Engineering (ENG) , 2015, DOI: 10.4236/eng.2015.710056
Abstract: Increasing complexity of today’s software systems is one of the major challenges software engineers have to face. This is aggravated by the fact that formerly isolated systems have to be interconnected to more complex systems, called System-of-Systems (SoS). Those systems are in charge to provide more functionality to the user than all of their independent sub-systems could do. Reducing the complexity of such systems is one goal of the software engineering paradigm called component-based software engineering (CBSE). CBSE enables the developers to treat individual sub-systems as components which interact via interfaces with a simulated environment. Thus those components can be developed and implemented independently from other components. After the implementation a system integrator is able to interconnect the components to a SoS. Despite this much-used approach it is possible to show that constraints, which are valid in an isolated sub-system, are broken after this system is integrated into a SoS. To emphasize this issue we developed a technique based on interconnected timed automata for modelling sub-systems and System-of-Systems in the model checking tool UPPAAL. The presented modelling technique allows it to verify the correctness of single sub-systems as well as the resulting SoS. Additionally we developed a tool which abstracts the complicated timed automata to an easy to read component based language with the goal to help system integrators building and verifying complex SoS.
Lipophilic Optical Supramolecular Nano Devices in the Aqueous Phase  [PDF]
Heinz Langhals, Tim Pust
Green and Sustainable Chemistry (GSC) , 2011, DOI: 10.4236/gsc.2011.11001
Abstract: Nano micelles of sodium dodecyl sulphate in water were prepared as local lipophilic media for the organisation of interacting chromophores. Such arrangements were controlled by peripheric substituents to operate either as isolated chromophores or as skew oriented pairs where H-type transitions cause hysochromic absorption and J-type transitions bathochromic fluorescence. As a consequence, large Stokes' shift could be obtained.
Aspects of Replayability and Software Engineering: Towards a Methodology of Developing Games  [PDF]
Joseph Krall, Tim Menzies
Journal of Software Engineering and Applications (JSEA) , 2012, DOI: 10.4236/jsea.2012.57052
Abstract: One application of software engineering is the vast and widely popular video game entertainment industry. Success of a video game product depends on how well the player base receives it. Of research towards understanding factors of success behind releasing a video game, we are interested in studying a factor known as Replayability. Towards a software engineering oriented game design methodology, we collect player opinions on Replayability via surveys and provide methods to analyze the data. We believe these results can help game designers to more successfully produce entertaining games with longer lasting appeal by utilizing our software engineering techniques.
Suprafibrillar structures of collagen, evidence for local organization and auxetic behaviour in architectures  [PDF]
Kate Patten, Tim Wess
Journal of Biophysical Chemistry (JBPC) , 2013, DOI: 10.4236/jbpc.2013.43014
Abstract: The suprafibrillar organisation of collagen rich tissues is the keystone to the diversity of resultant structures made from relatively similar materials. The local organisation between fibrils may be essential to suprafibril structures that are critical to functionality such as transparency in cornea, where specific lateral relationships between fibrils dictate optical properties. Here we show that corneal X-ray diffraction combined with mechanical strains to disrupt a specific suprafibrillar relationship between fibrils evidence and a coherent staggered axial relationship between collagen fibrils. The data also shows evidence for auxetic behavior of the collagen fibrils and reveals a 120 nm diffraction feature previously unreported in collagen tissues. The results show that suprafibrillar organisation can be an essential component in tissue architecture that has hitherto been ignored, but now must be considered in mechanical and structural models.
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