The Experts below are selected from a list of 33252 Experts worldwide ranked by ideXlab platform

Cao Yiyu - One of the best experts on this subject based on the ideXlab platform.

  • Predicting Caco-2 permeability using support vector machine and chemistry Development Kit
    J Pharm Pharm Sci, 2006
    Co-Authors: M Guangli, Cao Yiyu
    Abstract:

    PURPOSE: To predict Caco-2 permeability is a valuable target for pharmaceutical research. Most of the Caco-2 prediction models are based on commercial or special software which limited their practical value. This study represents the relationship between Caco-2 permeability and molecular descriptors totally based on open source software. METHODS:The Caco-2 prediction model was constructed based on descriptors generated by open source software Chemistry Development Kit (CDK) and a support vector machine (SVM) method. Number of H-bond donors and three molecular surface area descriptors constructed the prediction model. RESULTS:The correlation coefficients (r) of the experimental and predicted Caco-2 apparent permeability for the training set and the test set were 0.88 and 0.85, respectively. CONCLUSION: The results suggest that the SVM method is effective for predicting Caco-2 permeability. Membrane permeability of compounds is determined by number of H-bond donors and molecular surface area properties.

  • Using Support Vector Machine and Chemistry Development Kit
    2006
    Co-Authors: M Guangli, Cao Yiyu
    Abstract:

    PURPOSE: To predict Caco-2 permeability is a valuable target for pharmaceutical research. Most of the Caco-2 prediction models are based on commercial or special software which limited their practical value. This study represents the relationship between Caco-2 permeability and molecular descriptors totally based on open source software. METHODS: The Caco-2 prediction model was constructed based on descriptors generated by open source software Chemistry Development Kit (CDK) and a support vector machine (SVM) method. Number of H-bond donors and three molecular surface area descriptors constructed the prediction model. RESULTS: The correlation coefficients (r) of the experimental and predicted Caco-2 apparent permeability for the training set and the test set were 0.88 and 0.85, respectively. CONCLUSIONS: The results suggest that the SVM method is effective for predicting Caco-2 permeability. Membrane permeability of compounds is determined by number of H-bond donors and molecular surface area properties.

Alexey Khabalov - One of the best experts on this subject based on the ideXlab platform.

  • CEEMAS - Software Development Kit for Multi-agent Systems Design and Implementation
    From Theory to Practice in Multi-Agent Systems, 2002
    Co-Authors: Vladimir I Gorodetski, Oleg Karsayev, Igor Kotenko, Alexey Khabalov
    Abstract:

    The paper presents the developed technology and software tool for design and implementation of knowledge-based multi-agent systems. The software tool comprises two components that are "Generic Agent- and "Multi-agent System Development Kit" (MAS DK). The former comprises reusable Visual C++ and Java classes and generic data and knowledge base structures, whereas the latter comprises several developer-friendly editors aimed at formal specification of the applied multi-agent system (MAS) under Development and installation of the resulting application in particular computer network environment. The developed technology and MAS DK were used in the design and implementation of the MAS prototype for computer network assurance and intrusion detection and distributed attack simulator. Several other applications are currently under Development.

  • software Development Kit for multi agent systems design and implementation
    Lecture Notes in Computer Science, 2002
    Co-Authors: Vladimir I Gorodetski, Oleg Karsayev, Igor Kotenko, Alexey Khabalov
    Abstract:

    The paper presents the developed technology and software tool for design and implementation of knowledge-based multi-agent systems. The software tool comprises two components that are Generic Agent and Multi-agent System Development Kit (MAS DK). The former comprises reusable Visual C++ and Java classes and generic data and knowledge base structures, whereas the latter comprises several developer-friendly editors aimed at formal specification of the applied multi-agent system (MAS) under Development and installation of the resulting application in particular computer network environment. The developed technology and MAS DK were used in the design and implementation of the MAS prototype for computer network assurance and intrusion detection and distributed attack simulator. Several other applications are currently under Development.

Egon Willighagen - One of the best experts on this subject based on the ideXlab platform.

  • the chemistry Development Kit cdk v2 0 atom typing depiction molecular formulas and substructure searching
    Journal of Cheminformatics, 2017
    Co-Authors: Egon Willighagen, John W Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomas Pluskal, Miquel Rojascherto, Ola Spjuth
    Abstract:

    Background: The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolKit, providing data structures to represent chemical concepts along with methods to manipulate such ...

  • The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching
    Journal of Cheminformatics, 2017
    Co-Authors: Egon Willighagen, John W Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomas Pluskal, Miquel Rojas-chertó, Ola Spjuth
    Abstract:

    Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolKit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. Results We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. Conclusions This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance

  • recent Developments of the chemistry Development Kit cdk an open source java library for chemo and bioinformatics
    Current Pharmaceutical Design, 2006
    Co-Authors: Christoph Steinbeck, Stefan Kuhn, Christian Hoppe, Matteo Floris, Rajarshi Guha, Egon Willighagen
    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 CDKs new QSAR capabilities and the recently introduced interface to statistical software.

  • the chemistry Development Kit cdk an open source java library for chemo and bioinformatics
    Journal of Chemical Information and Computer Sciences, 2003
    Co-Authors: Christoph Steinbeck, Stefan Kuhn, Yongquan Han, Oliver Horlacher, Edgar Luttmann, Egon Willighagen
    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 access information for interested users and potential contributors are given.

Vladimir I Gorodetski - One of the best experts on this subject based on the ideXlab platform.

  • Intelligent Information Processing - Multi-agent system Development Kit: MAS software tool implementing Gaia methodology
    Intelligent Information Processing II, 2005
    Co-Authors: Vladimir I Gorodetski, Oleg Karsaev, Vladimir Samoilov, Victor Konushy, Evgeny Mankov, Alexey Malyshev
    Abstract:

    Recent research in area of multi-agent technology attracted a growing attention of both scientific community and industrial companies. This attention is stipulated by powerful capabilities of multi-agent technology allowing to create large scale distributed intelligent systems, and, on the other hand, by practical needs of industrial companies to possess an advanced and reliable technology for solving of practically important problems. Currently one of the topmost questions of the research is Development of powerful methodologies for engineering of agent-based systems and Development of more effective and efficient tools supporting implementation of applied systems. The paper presents one of such tools, Multi Agent System Development Kit, based on and implementing of Gaia methodology. It supports the whole life cycle of multi-agent system Development and maintains integrity of solutions produced at different stages of the Development process.

  • CEEMAS - Software Development Kit for Multi-agent Systems Design and Implementation
    From Theory to Practice in Multi-Agent Systems, 2002
    Co-Authors: Vladimir I Gorodetski, Oleg Karsayev, Igor Kotenko, Alexey Khabalov
    Abstract:

    The paper presents the developed technology and software tool for design and implementation of knowledge-based multi-agent systems. The software tool comprises two components that are "Generic Agent- and "Multi-agent System Development Kit" (MAS DK). The former comprises reusable Visual C++ and Java classes and generic data and knowledge base structures, whereas the latter comprises several developer-friendly editors aimed at formal specification of the applied multi-agent system (MAS) under Development and installation of the resulting application in particular computer network environment. The developed technology and MAS DK were used in the design and implementation of the MAS prototype for computer network assurance and intrusion detection and distributed attack simulator. Several other applications are currently under Development.

  • software Development Kit for multi agent systems design and implementation
    Lecture Notes in Computer Science, 2002
    Co-Authors: Vladimir I Gorodetski, Oleg Karsayev, Igor Kotenko, Alexey Khabalov
    Abstract:

    The paper presents the developed technology and software tool for design and implementation of knowledge-based multi-agent systems. The software tool comprises two components that are Generic Agent and Multi-agent System Development Kit (MAS DK). The former comprises reusable Visual C++ and Java classes and generic data and knowledge base structures, whereas the latter comprises several developer-friendly editors aimed at formal specification of the applied multi-agent system (MAS) under Development and installation of the resulting application in particular computer network environment. The developed technology and MAS DK were used in the design and implementation of the MAS prototype for computer network assurance and intrusion detection and distributed attack simulator. Several other applications are currently under Development.

M Guangli - One of the best experts on this subject based on the ideXlab platform.

  • Predicting Caco-2 permeability using support vector machine and chemistry Development Kit
    J Pharm Pharm Sci, 2006
    Co-Authors: M Guangli, Cao Yiyu
    Abstract:

    PURPOSE: To predict Caco-2 permeability is a valuable target for pharmaceutical research. Most of the Caco-2 prediction models are based on commercial or special software which limited their practical value. This study represents the relationship between Caco-2 permeability and molecular descriptors totally based on open source software. METHODS:The Caco-2 prediction model was constructed based on descriptors generated by open source software Chemistry Development Kit (CDK) and a support vector machine (SVM) method. Number of H-bond donors and three molecular surface area descriptors constructed the prediction model. RESULTS:The correlation coefficients (r) of the experimental and predicted Caco-2 apparent permeability for the training set and the test set were 0.88 and 0.85, respectively. CONCLUSION: The results suggest that the SVM method is effective for predicting Caco-2 permeability. Membrane permeability of compounds is determined by number of H-bond donors and molecular surface area properties.

  • Using Support Vector Machine and Chemistry Development Kit
    2006
    Co-Authors: M Guangli, Cao Yiyu
    Abstract:

    PURPOSE: To predict Caco-2 permeability is a valuable target for pharmaceutical research. Most of the Caco-2 prediction models are based on commercial or special software which limited their practical value. This study represents the relationship between Caco-2 permeability and molecular descriptors totally based on open source software. METHODS: The Caco-2 prediction model was constructed based on descriptors generated by open source software Chemistry Development Kit (CDK) and a support vector machine (SVM) method. Number of H-bond donors and three molecular surface area descriptors constructed the prediction model. RESULTS: The correlation coefficients (r) of the experimental and predicted Caco-2 apparent permeability for the training set and the test set were 0.88 and 0.85, respectively. CONCLUSIONS: The results suggest that the SVM method is effective for predicting Caco-2 permeability. Membrane permeability of compounds is determined by number of H-bond donors and molecular surface area properties.