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Journal of cheminformatics, Vol. 2, No. 1. (30 June 2010), 5.
Abstract
ABSTRACT: BACKGROUND: QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the ...
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BMC Bioinformatics, Vol. 10, No. 1. (2009), 279.
Abstract
BACKGROUND:Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send ...
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BMC bioinformatics, Vol. 11, No. 1. (29 March 2010), 159.
Abstract
BACKGROUND: Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools to process them and discover new knowledge. To freely support open science based on these data resources, it is desirable for the processing tools to be open source and available for everyone. RESULTS: Here we describe a novel combination of the workflow engine Taverna and the cheminformatics library Chemistry ...
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CEUR Workshop Proceedings In SWAT4LS-2009 - Semantic Web Applications and Tools for Life Sciences, Vol. 559 (2010)
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Nature Precedings, No. 713. (14 June 2007)
Abstract
Jmol is a free, open source molecule viewer for chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts: the JmolApplet is a web browser applet that can be integrated into web pages; the Jmol application is a standalone Java application that runs on the desktop; and the JmolViewer is a development tool kit that can be integrated into other Java applications. ...
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BMC bioinformatics, Vol. 10, No. 1. (3 December 2009), 397.
by Ola Spjuth, Jonathan Alvarsson, Arvid Berg, et al.Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain Torrance, Johannes Wagener, Egon L. Willighagen, Christoph Steinbeck, Jarl E. Wikberg
Abstract
BACKGROUND: Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks. RESULTS: Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both ...
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Crystal Growth & Design, Vol. 7, No. 9. (1 September 2007), pp. 1738-1745.
Abstract
Supervised self-organizing maps (SOMs) provide a new method to explore large numbers of crystal structures and to visualize structureproperty relationships. Examples show how powder diffraction patterns and one or more structural properties determine the positions of crystal structures on the supervised SOMs, and show that the maps allow the classification of structures, prediction of properties, and subset selection in polymorph prediction. ...
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In Handbook of Chemoinformatics Algorithms (2010)
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RNews, Vol. 6, No. 3. (2006), pp. 24-28.
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In Proceedings of UK e-Science All Hands Meeting 2004, Vol. 1 (2004), pp. 930-933.
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In Proceedings of the 2003 UK e-Science All Hands Meeting (2003)
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European Journal of Organic Chemistry, Vol. 2002, No. 8. (2002), pp. 1397-1406.
Abstract
The synthesis of three novel cationic gemini surfactants (10, 12, and 14) based on tartaric acid appended with biocompatible palmitoyl tails and head groups is described, and their aggregation in water, monolayer behaviour, DNA binding, and gene transfection activities are reported. The monolayer studies showed that the molecular area of the surfactants is determined by the head group, as it increased going from the ethylenediamine head group of 10 via the lysine head group of 12 to the combined lysine/ethylenediamine head ...
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Journal of chemical information and modeling, Vol. 47, No. 6. (c 2007), pp. 2015-2034.
Abstract
CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist. ...
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BMC Bioinformatics, Vol. 8, No. 1. (2007), 487.
Abstract
BACKGROUND:The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework ...
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Nature Preceedings
Abstract
Jmol is a free, open source molecule viewer for chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts: the JmolApplet is a web browser applet that can be integrated into web pages; the Jmol application is a standalone Java application that runs on the desktop; and the JmolViewer is a development tool kit that can be integrated into other Java applications. ...
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Critical Reviews in Analytical Chemistry, No. 3. (2006), pp. 189-198.
Abstract
This paper reviews literature from the past 5 years in the field of molecular chemometrics, which applies modeling and data analysis to molecular data. It discusses advances and standing challenges in the fields of molecular representation, similarity and diversity analysis, quantitative structure-activity and structure-property relationship modeling, and library searching. ...
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Molecules, Vol. 5 (2000), pp. 93-98.
Abstract
The open source program for drawing 2D chemical structures JChemPaint, its current features, its envisioned further development and the principles enabling researchers and students at places all over the world to collaboratively develop such a program are described. ...
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Internet Journal of Chemistry, Vol. 4 (2001), 4.
Abstract
This article describes the first opensource Java implementation of import filters for the Chemical Markup Language (CML). The filters support CML conventions and were tested with two opensource project: Jmol, a 3D molecular viewer, and JChemPaint, a chemical editor. Furthermore, the use of conventions in CML is explained and the reason for using conventions is pointed out. Finally, the implementation is compared with two recently developed techniques for handling CML data. ...
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J Chem Inf Comput Sci, Vol. 43, No. 2. (r 2003), pp. 493-500.
Abstract
The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Application scenarios as well as ...
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J Chem Inf Comput Sci, Vol. 44, No. 2. (r 2004), pp. 462-469.
Abstract
Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information. ...
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Acta Crystallographica Section B, Vol. B61 (2005), pp. 29-36.
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J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 487-494.
Abstract
Recently, 1D NMR and IR spectra have been proposed as descriptors containing 3D information. And, as such, said to be suitable for making QSAR and QSPR models where 3D molecular geometries matter, for example, in binding affinities. This paper presents a study on the predictive power of 1D NMR spectra-based QSPR models using simulated proton and carbon 1D NMR spectra. It shows that the spectra-based models are outperformed by models based on theoretical molecular descriptors and that spectra-based models are not ...
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Current pharmaceutical design, Vol. 12, No. 17. (2006), pp. 2111-2120.
Abstract
The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software. ...
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BMC bioinformatics, Vol. 8, No. 1. (2007)
Abstract
BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no ...
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Journal of Chemical Information and Modeling, Vol. 46, No. 3. (1 May 2006), pp. 991-998.
Abstract
The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for ...
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