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T. Schwede - One of the best experts on this subject based on the ideXlab platform.

  • automated comparative protein structure Modeling with swiss Model and swiss pdbviewer a historical perspective
    Electrophoresis, 2009
    Co-Authors: Nicolas Guex, T. Schwede, Manuel C Peitsch
    Abstract:

    SWISS-Model pioneered the field of automated Modeling as the first protein Modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-Model Repository, it provides a fully integrated sequence to structure analysis and Modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein Modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.

  • The SWISS-Model Repository and associated resources
    Nucleic Acids Research, 2009
    Co-Authors: F. Kiefer, K. Arnold, M. Kunzli, L. Bordoli, T. Schwede
    Abstract:

    SWISS-Model Repository (http://swissModel.expasy.org/Repository/) is a database of 3D protein structure Models generated by the SWISS-Model homology-Modelling pipeline. The aim of the SWISS-Model Repository is to provide access to an up-to-date collection of annotated 3D protein Models generated by automated homology Modelling for all sequences in Swiss-Prot and for relevant Models organisms. Regular updates ensure that target coverage is complete, that Models are built using the most recent sequence and template structure databases, and that improvements in the underlying Modelling pipeline are fully utilised. As of September 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. SWISS-Model Repository allows the users to assess the quality of the Models in the database, search for alternative template structures, and to build Models interactively via SWISS-Model Workspace (http://swissModel.expasy.org/workspace/). Annotation of Models with functional information and cross-linking with other databases such as the Protein Model Portal (http://www.proteinModelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources

  • The SWISS-Model Repository: new features and functionalities.
    Nucleic acids research, 2006
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    The SWISS-Model Repository is a database of annotated 3D protein structure Models generated by the SWISS-Model homology-Modelling pipeline. As of September 2005, the Repository contained 675,000 Models for 604,000 different protein sequences of the UniProt database. Regular updates ensure that the content of the Repository reflects the current state of sequence and structure databases, integrating new or modified target sequences, and making use of new template structures. Each Repository entry consists of one or more 3D Models accompanied by detailed information about the target protein and the Model building process: functional annotation, a detailed template selection log, target-template alignment, summary of the Model building and Model quality assessment. The SWISS-Model Repository is freely accessible at http://swissModel.expasy.org/Repository/.

  • The SWISS-Model Repository: new features and functionalities
    Nucleic Acids Research, 2006
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    SWISS-Model Repository (SMR) is a database of annotated 3D protein structure Models generated by the automated SWISS-Model homology Modeling pipeline. It currently holds >400 000 high quality Models covering almost 20% of Swiss-Prot/UniProtKB entries. In this manuscript, we provide an update of features and functionalities which have been implemented recently. We address improvements in target coverage, Model quality estimates, functional annotations and improved in-page visualization. We also introduce a new update concept which includes regular updates of an expanded set of core organism Models and UniProtKB-based targets, complemented by user-driven on-demand update of individual Models. With the new release of the Modeling pipeline, SMR has implemented a REST-API and adopted an open licencing Model for accessing Model coordinates, thus enabling bulk download for groups of targets fostering re-use of Models in other contexts. SMR can be accessed at https://swissModel.expasy.org/Repository.

  • the swiss Model Repository of annotated three dimensional protein structure homology Models
    Nucleic Acids Research, 2004
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    The SWISS-Model Repository is a database of annotated three-dimensional comparative protein structure Models generated by the fully automated homology-Modelling pipeline SWISS-Model. The Repository currently contains about 300,000 three-dimensional Models for sequences from the Swiss-Prot and TrEMBL databases. The content of the Repository is updated on a regular basis incorporating new sequences, taking advantage of new template structures becoming available and reflecting improvements in the underlying Modelling algorithms. Each entry consists of one or more three-dimensional protein Models, the superposed template structures, the alignments on which the Models are based, a summary of the Modelling process and a force field based quality assessment. The SWISS-Model Repository can be queried via an interactive website at http://swissModel.expasy. org/Repository/. Annotation and cross-linking of the Models with other databases, e.g. Swiss-Prot on the ExPASy server, allow for seamless navigation between protein sequence and structure information. The aim of the SWISS-Model Repository is to provide access to an up-to-date collection of annotated three-dimensional protein Models generated by automated homology Modelling, bridging the gap between sequence and structure databases.

Manuel C Peitsch - One of the best experts on this subject based on the ideXlab platform.

  • automated comparative protein structure Modeling with swiss Model and swiss pdbviewer a historical perspective
    Electrophoresis, 2009
    Co-Authors: Nicolas Guex, T. Schwede, Manuel C Peitsch
    Abstract:

    SWISS-Model pioneered the field of automated Modeling as the first protein Modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-Model Repository, it provides a fully integrated sequence to structure analysis and Modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein Modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.

  • large scale protein Modeling and Model Repository
    Intelligent Systems in Molecular Biology, 1997
    Co-Authors: Manuel C Peitsch
    Abstract:

    Knowledge-based molecular Modelling of proteins has proven useful in many instances including the rational design of mutagenesis experiments, but it has been generally limited by the availability of expensive computer hardware and software. To overcome these limitations, we have developed the SWISS-Model server for automated knowledge-based protein Modelling. The SWISS-Model server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein Models for sequences which share significant similarities with at least one protein of known 3D-structure. We now use the software framework of the server to generate large collections of protein Models. To store these Models, we have established the SWISS-Model Repository, a new database for protein Models generated by theoretical approaches. This Repository is directly integrated with SWISS-PROT and other databases through the ExPASy World-Wide Web server (URL is http://www.expasy.ch).

  • ISMB - Large Scale Protein Modeling and Model Repository
    Proceedings. International Conference on Intelligent Systems for Molecular Biology, 1997
    Co-Authors: Manuel C Peitsch
    Abstract:

    Knowledge-based molecular Modelling of proteins has proven useful in many instances including the rational design of mutagenesis experiments, but it has been generally limited by the availability of expensive computer hardware and software. To overcome these limitations, we have developed the SWISS-Model server for automated knowledge-based protein Modelling. The SWISS-Model server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein Models for sequences which share significant similarities with at least one protein of known 3D-structure. We now use the software framework of the server to generate large collections of protein Models. To store these Models, we have established the SWISS-Model Repository, a new database for protein Models generated by theoretical approaches. This Repository is directly integrated with SWISS-PROT and other databases through the ExPASy World-Wide Web server (URL is http://www.expasy.ch).

  • swiss Model and the swiss pdb viewer an environment for comparative protein Modeling
    Electrophoresis, 1997
    Co-Authors: Nicolas Gue, Manuel C Peitsch
    Abstract:

    Comparative protein Modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting Models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein Modeling that consists of SWISS-Model, a server for automated comparative protein Modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-Model, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-Model Repository, a database containing more than 3500 automatically generated protein Models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and Models in the process of experiment design.

  • swiss Model and the swiss pdbviewer an environment for comparative protein Modeling
    Electrophoresis, 1997
    Co-Authors: Nicolas Guex, Manuel C Peitsch
    Abstract:

    Comparative protein Modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting Models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein Modeling that consists of SWISS-Model, a server for automated comparative protein Modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-Model, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-Model Repository, a database containing more than 3500 automatically generated protein Models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and Models in the process of experiment design.

J. Kopp - One of the best experts on this subject based on the ideXlab platform.

  • The SWISS-Model Repository: new features and functionalities
    Nucleic Acids Research, 2006
    Co-Authors: J. Kopp
    Abstract:

    The SWISS-Model Repository is a database of annotated 3D protein structure Models generated by the SWISS-Model homology-Modelling pipeline. As of September 2005, the Repository contained 675 000 Models for 604 000 different protein sequences of the UniProt database. Regular updates ensure that the content of the Repository reflects the current state of sequence and structure databases, integrating new or modified target sequences, and making use of new template structures. Each Repository entry consists of one or more 3D Models accompanied by detailed information about the target protein and the Model building process: functional annotation, a detailed template selection log, target-template alignment, summary of the Model building and Model quality assessment. The SWISS-Model Repository is freely accessible at

  • The SWISS-Model Repository: new features and functionalities.
    Nucleic acids research, 2006
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    The SWISS-Model Repository is a database of annotated 3D protein structure Models generated by the SWISS-Model homology-Modelling pipeline. As of September 2005, the Repository contained 675,000 Models for 604,000 different protein sequences of the UniProt database. Regular updates ensure that the content of the Repository reflects the current state of sequence and structure databases, integrating new or modified target sequences, and making use of new template structures. Each Repository entry consists of one or more 3D Models accompanied by detailed information about the target protein and the Model building process: functional annotation, a detailed template selection log, target-template alignment, summary of the Model building and Model quality assessment. The SWISS-Model Repository is freely accessible at http://swissModel.expasy.org/Repository/.

  • The SWISS-Model Repository: new features and functionalities
    Nucleic Acids Research, 2006
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    SWISS-Model Repository (SMR) is a database of annotated 3D protein structure Models generated by the automated SWISS-Model homology Modeling pipeline. It currently holds >400 000 high quality Models covering almost 20% of Swiss-Prot/UniProtKB entries. In this manuscript, we provide an update of features and functionalities which have been implemented recently. We address improvements in target coverage, Model quality estimates, functional annotations and improved in-page visualization. We also introduce a new update concept which includes regular updates of an expanded set of core organism Models and UniProtKB-based targets, complemented by user-driven on-demand update of individual Models. With the new release of the Modeling pipeline, SMR has implemented a REST-API and adopted an open licencing Model for accessing Model coordinates, thus enabling bulk download for groups of targets fostering re-use of Models in other contexts. SMR can be accessed at https://swissModel.expasy.org/Repository.

  • the swiss Model Repository of annotated three dimensional protein structure homology Models
    Nucleic Acids Research, 2004
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    The SWISS-Model Repository is a database of annotated three-dimensional comparative protein structure Models generated by the fully automated homology-Modelling pipeline SWISS-Model. The Repository currently contains about 300,000 three-dimensional Models for sequences from the Swiss-Prot and TrEMBL databases. The content of the Repository is updated on a regular basis incorporating new sequences, taking advantage of new template structures becoming available and reflecting improvements in the underlying Modelling algorithms. Each entry consists of one or more three-dimensional protein Models, the superposed template structures, the alignments on which the Models are based, a summary of the Modelling process and a force field based quality assessment. The SWISS-Model Repository can be queried via an interactive website at http://swissModel.expasy. org/Repository/. Annotation and cross-linking of the Models with other databases, e.g. Swiss-Prot on the ExPASy server, allow for seamless navigation between protein sequence and structure information. The aim of the SWISS-Model Repository is to provide access to an up-to-date collection of annotated three-dimensional protein Models generated by automated homology Modelling, bridging the gap between sequence and structure databases.

  • The SWISS‐Model Repository of annotated three‐dimensional protein structure homology Models
    Nucleic Acids Research, 2004
    Co-Authors: J. Kopp, T. Schwede
    Abstract:

    The SWISS-Model Repository is a database of annotated three-dimensional comparative protein structure Models generated by the fully automated homology-Modelling pipeline SWISS-Model. The Repository currently contains about 300,000 three-dimensional Models for sequences from the Swiss-Prot and TrEMBL databases. The content of the Repository is updated on a regular basis incorporating new sequences, taking advantage of new template structures becoming available and reflecting improvements in the underlying Modelling algorithms. Each entry consists of one or more three-dimensional protein Models, the superposed template structures, the alignments on which the Models are based, a summary of the Modelling process and a force field based quality assessment. The SWISS-Model Repository can be queried via an interactive website at http://swissModel.expasy. org/Repository/. Annotation and cross-linking of the Models with other databases, e.g. Swiss-Prot on the ExPASy server, allow for seamless navigation between protein sequence and structure information. The aim of the SWISS-Model Repository is to provide access to an up-to-date collection of annotated three-dimensional protein Models generated by automated homology Modelling, bridging the gap between sequence and structure databases.

Brahim Hamid - One of the best experts on this subject based on the ideXlab platform.

  • A Model-driven approach for developing a Model Repository: Methodology and tool support
    Future Generation Computer Systems, 2017
    Co-Authors: Brahim Hamid
    Abstract:

    Several development approaches have been proposed to cope with the increasing complexity of embedded system design. The most widely used approaches are those using Models as the main artifacts to be constructed and maintained. The desired role of Models is to ease, systematize and standardize the approach to the construction of software-based systems. To enforce reuse and interconnect the process of Model specification and system development with Models, we promote a Model-based approach coupled with a Model Repository. In this paper, we propose a Model-driven engineering methodological approach for the development of a Model Repository and an operational architecture for development tools. In addition, we provide evidence of the benefits and feasibility of our approach by reporting on a preliminary prototype that provides a Model-based Repository of security and dependability (S&D) pattern Models. Finally, we apply the proposed approach in practice to a use case from the railway domain with strong S&D requirements.

  • ICSR - A Model Repository Description Language - MRDL
    Lecture Notes in Computer Science, 2016
    Co-Authors: Brahim Hamid
    Abstract:

    Repository-based development of software systems has gained more attention recently by addressing new challenges such as security and dependability. However, there are still gaps in existing Modeling languages and/or formalisms dedicated to define Model repositories and the way how to reuse them in the automation of software development. Thus, there is a strong requirement for defining a Model Repository description language not only as a Modeling approach, but also as a suitable instrument to support system and software engineers in the activity of search and retrieval of appropriate Models beyond keyword-based search. Moreover, Modeling approaches allow using tools for the specification and the exploitation of the designed artifacts e.g. analysis and evaluation. The goal of this paper is to advance the state of the art in Model Repository description for software and systems engineering. In particular, we have designed a flexible and extensible Modeling language, by means of an OMG style metaModel, to specify Model repositories for Modeling artifacts, and we have defined an operational architecture for development tools. In particular, we show the feasibility of our own approach by reporting some preliminary prototype providing a Model-based Repository of security and dependability S&D pattern Models.

Nicolas Guex - One of the best experts on this subject based on the ideXlab platform.

  • automated comparative protein structure Modeling with swiss Model and swiss pdbviewer a historical perspective
    Electrophoresis, 2009
    Co-Authors: Nicolas Guex, T. Schwede, Manuel C Peitsch
    Abstract:

    SWISS-Model pioneered the field of automated Modeling as the first protein Modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-Model Repository, it provides a fully integrated sequence to structure analysis and Modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein Modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.

  • swiss Model and the swiss pdbviewer an environment for comparative protein Modeling
    Electrophoresis, 1997
    Co-Authors: Nicolas Guex, Manuel C Peitsch
    Abstract:

    Comparative protein Modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting Models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein Modeling that consists of SWISS-Model, a server for automated comparative protein Modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-Model, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-Model Repository, a database containing more than 3500 automatically generated protein Models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and Models in the process of experiment design.