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  1. Article ; Online: CCP4i2: the new graphical user interface to the CCP4 program suite.

    Potterton, Liz / Agirre, Jon / Ballard, Charles / Cowtan, Kevin / Dodson, Eleanor / Evans, Phil R / Jenkins, Huw T / Keegan, Ronan / Krissinel, Eugene / Stevenson, Kyle / Lebedev, Andrey / McNicholas, Stuart J / Nicholls, Robert A / Noble, Martin / Pannu, Navraj S / Roth, Christian / Sheldrick, George / Skubak, Pavol / Turkenburg, Johan /
    Uski, Ville / von Delft, Frank / Waterman, David / Wilson, Keith / Winn, Martyn / Wojdyr, Marcin

    Acta crystallographica. Section D, Structural biology

    2018  Volume 74, Issue Pt 2, Page(s) 68–84

    Abstract: The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate ... ...

    Abstract The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.
    MeSH term(s) Computer Graphics ; Crystallography, X-Ray/instrumentation ; Crystallography, X-Ray/methods ; Macromolecular Substances/chemistry ; Molecular Structure ; Proteins/chemistry ; Software ; User-Computer Interface
    Chemical Substances Macromolecular Substances ; Proteins
    Language English
    Publishing date 2018-02-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798317016035
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.

    Vagin, Alexei A / Steiner, Roberto A / Lebedev, Andrey A / Potterton, Liz / McNicholas, Stuart / Long, Fei / Murshudov, Garib N

    Acta crystallographica. Section D, Biological crystallography

    2004  Volume 60, Issue Pt 12 Pt 1, Page(s) 2184–2195

    Abstract: One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution ... ...

    Abstract One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.
    MeSH term(s) Chemical Phenomena ; Chemistry ; Computational Biology ; Crystallography, X-Ray ; Dictionaries as Topic ; Internet ; Models, Molecular ; Peptide Library ; Protein Conformation ; Proteins/chemistry ; Software
    Chemical Substances Peptide Library ; Proteins
    Language English
    Publishing date 2004-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020492-9
    ISSN 2059-7983 ; 1399-0047 ; 0907-4449
    ISSN (online) 2059-7983 ; 1399-0047
    ISSN 0907-4449
    DOI 10.1107/S0907444904023510
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Developments in the CCP4 molecular-graphics project.

    Potterton, Liz / McNicholas, Stuart / Krissinel, Eugene / Gruber, Jan / Cowtan, Kevin / Emsley, Paul / Murshudov, Garib N / Cohen, Serge / Perrakis, Anastassis / Noble, Martin

    Acta crystallographica. Section D, Biological crystallography

    2004  Volume 60, Issue Pt 12 Pt 1, Page(s) 2288–2294

    Abstract: Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances ... ...

    Abstract Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.
    MeSH term(s) Algorithms ; Computer Graphics ; Crystallography, X-Ray ; Electrons ; Ligands ; Models, Molecular ; Nucleic Acids/chemistry ; Peptide Library ; Protein Structure, Secondary ; Proteins/chemistry ; Software ; Static Electricity ; User-Computer Interface
    Chemical Substances Ligands ; Nucleic Acids ; Peptide Library ; Proteins
    Language English
    Publishing date 2004-11-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020492-9
    ISSN 1399-0047 ; 0907-4449
    ISSN (online) 1399-0047
    ISSN 0907-4449
    DOI 10.1107/S0907444904023716
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

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