The Experts below are selected from a list of 288 Experts worldwide ranked by ideXlab platform
Paul D. Adams - One of the best experts on this subject based on the ideXlab platform.
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phenix a comprehensive python based system for Macromolecular Structure solution
International Tables for Crystallography, 2012Co-Authors: Pavel V Afonine, Liwei Hung, Paul D. Adams, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Gabo Unkoczi, Vince Che, Gary J KapralAbstract:Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these Structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for Macromolecular crystallographic Structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. Keywords: PHENIX; Python; algorithms
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phenix a comprehensive python based system for Macromolecular Structure solution
Acta Crystallographica Section D-biological Crystallography, 2010Co-Authors: Gabor Bunkoczi, Pavel V Afonine, Vincent B Chen, Liwei Hung, Paul D. Adams, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Gary J KapralAbstract:Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these Structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for Macromolecular crystallographic Structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
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Recent developments in software for the automation of crystallographic Macromolecular Structure determination.
Current opinion in structural biology, 2000Co-Authors: Paul D. Adams, Ralf W. Grosse-kunstleveAbstract:The automation of Macromolecular Structure determination by X-ray crystallography has long been a goal for many researchers. Recently, there have been improvements in the underlying algorithms, some of which have been implemented in software packages that deal with multiple stages of the Structure determination process. These first steps towards complete automation have made X-ray crystallography more efficient.
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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Acta Crystallographica Section D Biological Crystallography, 1998Co-Authors: Axel T. Brunger, Michael Nilges, Paul D. Adams, G. M. Clore, W. L. Delano, Piet Gros, R.w. Grosse-kunstleve, Jiansheng Jiang, J. Kuszewski, Navraj S. PannuAbstract:A new software suite, called Crystallography & NMR System (CNS), has been developed for Macromolecular Structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing Structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other Structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical Structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic Structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data Structures, such as Structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of Macromolecular Structure determination by X-ray crystallography and solution NMR.
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crystallography nmr system a new software suite for Macromolecular Structure determination
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Axel T. Brunger, Paul D. Adams, G. M. Clore, W. L. Delano, Piet Gros, Jiansheng Jiang, R W Grossekunstleve, J. KuszewskiAbstract:A new software suite, called Crystallography & NMR System (CNS), has been developed for Macromolecular Structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing Structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other Structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical Structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic Structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data Structures, such as Structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of Macromolecular Structure determination by X-ray crystallography and solution NMR.
Zhifei Liu - One of the best experts on this subject based on the ideXlab platform.
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Macromolecular Structure Controlling Micro Mechanical Properties of Vitrinite and Inertinite in Tectonically Deformed Coals—A Case Study in Fengfeng Coal Mine of Taihangshan Fault Zone (North China)
Energies, 2020Co-Authors: Anmin Wang, Daiyong Cao, Yingchun Wei, Zhifei LiuAbstract:In order to study the evolution of the mechanical properties and Macromolecular Structures in different macerals of tectonically deformed coal (TDC), vitrinite and inertinite samples were handpicked from six block TDCs in the same coal seam with an increasing deformation degree (unaltered, cataclastic, porphyroclast, scaly and powdery coal). The micro mechanical properties were tested by the nanoindentation experiment and the Macromolecular Structures were measured using 13C nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR). The results show that the range of hardness and elastic modulus of inertinite is 0.373–1.517 GPa and 4.339–12.158 GPa, respectively, which is significantly higher than that of vitrinite with values of 0.278–0.456 GPa and 4.857–7.810 GPa, respectively. From unaltered coal to powdery coal, the hardness of vitrinite and inertinite gradually decreases, with the difference between these macerals becomes smaller and the elastic modulus of vitrinite shows an increasing trend, while that of inertinite was more variable. Both the NMR and FITR results reveal that the Macromolecular Structure of inertinite has similar structural transitions as vitrinite. As the degree of deformation increases, the aliphatic side chains become shorter and the aromaticity is increasing. Macromolecular alterations caused by tectonic stress is expected to produce defects in the TDCs, therefore there should be more interspacing among the Macromolecular groups for the extrusion of macromolecules caused by the indenter of the nanoindentation experiment, thereby reducing the hardness. The elastic modulus of coal is believed to be related to intermolecular forces, which are positively correlated to the dipole moment. By calculating the dipole moments of the typical aromatic molecular Structures with aliphatic side chains, the detachment of the aliphatic side chains and the growth of benzene rings can both increase the dipole moment, which can promote elastic modulus. In addition, the increasing number of benzene rings can create more π-π bonds between the molecules, which can lead to an increase in the intermolecular forces, further increasing the elastic modulus.
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Macromolecular Structure controlling micro mechanical properties of vitrinite and inertinite in tectonically deformed coals a case study in fengfeng coal mine of taihangshan fault zone north china
Energies, 2020Co-Authors: Anmin Wang, Daiyong Cao, Yingchun Wei, Zhifei LiuAbstract:In order to study the evolution of the mechanical properties and Macromolecular Structures in different macerals of tectonically deformed coal (TDC), vitrinite and inertinite samples were handpicked from six block TDCs in the same coal seam with an increasing deformation degree (unaltered, cataclastic, porphyroclast, scaly and powdery coal). The micro mechanical properties were tested by the nanoindentation experiment and the Macromolecular Structures were measured using 13C nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR). The results show that the range of hardness and elastic modulus of inertinite is 0.373–1.517 GPa and 4.339–12.158 GPa, respectively, which is significantly higher than that of vitrinite with values of 0.278–0.456 GPa and 4.857–7.810 GPa, respectively. From unaltered coal to powdery coal, the hardness of vitrinite and inertinite gradually decreases, with the difference between these macerals becomes smaller and the elastic modulus of vitrinite shows an increasing trend, while that of inertinite was more variable. Both the NMR and FITR results reveal that the Macromolecular Structure of inertinite has similar structural transitions as vitrinite. As the degree of deformation increases, the aliphatic side chains become shorter and the aromaticity is increasing. Macromolecular alterations caused by tectonic stress is expected to produce defects in the TDCs, therefore there should be more interspacing among the Macromolecular groups for the extrusion of macromolecules caused by the indenter of the nanoindentation experiment, thereby reducing the hardness. The elastic modulus of coal is believed to be related to intermolecular forces, which are positively correlated to the dipole moment. By calculating the dipole moments of the typical aromatic molecular Structures with aliphatic side chains, the detachment of the aliphatic side chains and the growth of benzene rings can both increase the dipole moment, which can promote elastic modulus. In addition, the increasing number of benzene rings can create more π-π bonds between the molecules, which can lead to an increase in the intermolecular forces, further increasing the elastic modulus.
Axel T. Brunger - One of the best experts on this subject based on the ideXlab platform.
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crystallography nmr system a new software suite for Macromolecular Structure determination
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Axel T. Brunger, Paul D. Adams, G. M. Clore, W. L. Delano, Piet Gros, Jiansheng Jiang, R W Grossekunstleve, J. KuszewskiAbstract:A new software suite, called Crystallography & NMR System (CNS), has been developed for Macromolecular Structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing Structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other Structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical Structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic Structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data Structures, such as Structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of Macromolecular Structure determination by X-ray crystallography and solution NMR.
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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Acta Crystallographica Section D Biological Crystallography, 1998Co-Authors: Axel T. Brunger, Michael Nilges, Paul D. Adams, G. M. Clore, W. L. Delano, Piet Gros, R.w. Grosse-kunstleve, Jiansheng Jiang, J. Kuszewski, Navraj S. PannuAbstract:A new software suite, called Crystallography & NMR System (CNS), has been developed for Macromolecular Structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing Structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other Structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical Structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic Structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data Structures, such as Structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of Macromolecular Structure determination by X-ray crystallography and solution NMR.
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Computational challenges for Macromolecular Structure determination by X-ray crystallography and solution NMRspectroscopy
Quarterly Reviews of Biophysics, 1993Co-Authors: Axel T. Brunger, Michael NilgesAbstract:Macromolecular Structure determination by X-ray crystallography and solution NMR spectroscopy has experienced unprecedented growth during the past decade.
Philip E. Bourne - One of the best experts on this subject based on the ideXlab platform.
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An ontology driven architecture for derived representations of Macromolecular Structure.
Bioinformatics (Oxford England), 2002Co-Authors: Douglas S. Greer, John D. Westbrook, Philip E. BourneAbstract:Summary: An object metamodel based on a standard scientific ontology has been developed and used to generate a CORBA interface, an SQL schema and an XML representation for Macromolecular Structure (MMS) data. In addition to the interface and schema definitions, the metamodel was also used to generate the core elements of a CORBA reference server and a JDBC database loader. The Java source code which implements this metamodel, the CORBA server, database loader and XML converter along with detailed documentation and code examples are available as part of the OpenMMS toolkit.
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STAR/mmCIF: An ontology for Macromolecular Structure
Bioinformatics (Oxford England), 2000Co-Authors: John D. Westbrook, Philip E. BourneAbstract:Motivation: Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final Structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing Macromolecular Structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of Macromolecular Structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less wellcharacterized data domains. Results: Details of the DDL, the dictionaries that have been developed, and software for reading and using this ontology are presented. Availability: Extensive documentation, software tools and the DDL and dictionaries are available from http:// ndbserver.rutgers.edu/ mmcif and associated mirror sites.
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star mmcif an ontology for Macromolecular Structure
Bioinformatics, 2000Co-Authors: John D. Westbrook, Philip E. BourneAbstract:Motivation: Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final Structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing Macromolecular Structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of Macromolecular Structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less wellcharacterized data domains. Results: Details of the DDL, the dictionaries that have been developed, and software for reading and using this ontology are presented. Availability: Extensive documentation, software tools and the DDL and dictionaries are available from http:// ndbserver.rutgers.edu/ mmcif and associated mirror sites.
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Macromolecular Structure databases past progress and future challenges
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Helge Weissig, Philip E. Bourne, Ilya N ShindyalovAbstract:Databases containing Macromolecular Structure data provide a crystallographer with important tools for use in solving, refining and understanding the functional significance of their protein Structures. Given this importance, this paper briefly summarizes past progress by outlining the features of the significant number of relevant databases developed to date. One recent database, PDB+, containing all current and obsolete Structures deposited with the Protein Data Bank (PDB) is discussed in more detail. PDB+ has been used to analyze the self-consistency of the current (1 January 1998) corpus of over 7000 Structures. A summary of those findings is presented (a full discussion will appear elsewhere) in the form of global and temporal trends within the data. These trends indicate that challenges exist if crystallographers are to provide the community with complete and consistent structural results in the future. It is argued that better information management practices are required to meet these challenges.
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ISMB - Code Generation through Annotation of Macromolecular Structure Data
Proceedings. International Conference on Intelligent Systems for Molecular Biology, 1997Co-Authors: John Biggs, Philip E. BourneAbstract:The maintenance of software which uses a rapidly evolving data annotation scheme is time consuming and expensive. At the same time without current software the annotation scheme itself becomes limited and is less likely to be widely adopted. A solution to this problem has been developed for the Macromolecular Crystallographic Information File (mmCIF) annotation scheme. The approach could generalized for a variety of annotation schemes used or proposed for molecular biology data. mmCIF provides a highly Structured and complete annotation for describing NMR and X-ray crystallographic data and the resulting maeromolecular Structures. This annotation is maintained in the mmCIF dictionary which on-rently contains over 3,200 terms. A major challenge is to maintain code for converting between mmCIF and Protein Data Bank (PDB) annotations while both continue to evolve. The solution has been to define a simple domain specific language (DSL) which added to the extensive annotation already found in the mmCIF dictionary. The DSL calls specific mapping modules for each category of data item in the mmCIF dictionary. Adding or changing the mapping between PDB and mmCIF items of data is slraighlforward since data categories (and hence mapping modules) correspond to elements of Macromolecular Structure familiar to the experimentalist. Each time a change is made to the macrornolecular annotation the appropriate change is made to the easily located and modifiable mapping modules. A code generator is then called which reads the mapping modules and creates a new executable for perfo~-ming the data conversion. In this way code is easily kept current by individuals with limited programming skill, but who have an understanding of Macromolecular Structure and details of the annotation scheme. Most important, the conversion process becomes part of the global dictionary and is not open to a variety of interpretations by different research groups writing code based on dictionary contents. Details of the DSL and code generator are provided.
Anmin Wang - One of the best experts on this subject based on the ideXlab platform.
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Macromolecular Structure Controlling Micro Mechanical Properties of Vitrinite and Inertinite in Tectonically Deformed Coals—A Case Study in Fengfeng Coal Mine of Taihangshan Fault Zone (North China)
Energies, 2020Co-Authors: Anmin Wang, Daiyong Cao, Yingchun Wei, Zhifei LiuAbstract:In order to study the evolution of the mechanical properties and Macromolecular Structures in different macerals of tectonically deformed coal (TDC), vitrinite and inertinite samples were handpicked from six block TDCs in the same coal seam with an increasing deformation degree (unaltered, cataclastic, porphyroclast, scaly and powdery coal). The micro mechanical properties were tested by the nanoindentation experiment and the Macromolecular Structures were measured using 13C nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR). The results show that the range of hardness and elastic modulus of inertinite is 0.373–1.517 GPa and 4.339–12.158 GPa, respectively, which is significantly higher than that of vitrinite with values of 0.278–0.456 GPa and 4.857–7.810 GPa, respectively. From unaltered coal to powdery coal, the hardness of vitrinite and inertinite gradually decreases, with the difference between these macerals becomes smaller and the elastic modulus of vitrinite shows an increasing trend, while that of inertinite was more variable. Both the NMR and FITR results reveal that the Macromolecular Structure of inertinite has similar structural transitions as vitrinite. As the degree of deformation increases, the aliphatic side chains become shorter and the aromaticity is increasing. Macromolecular alterations caused by tectonic stress is expected to produce defects in the TDCs, therefore there should be more interspacing among the Macromolecular groups for the extrusion of macromolecules caused by the indenter of the nanoindentation experiment, thereby reducing the hardness. The elastic modulus of coal is believed to be related to intermolecular forces, which are positively correlated to the dipole moment. By calculating the dipole moments of the typical aromatic molecular Structures with aliphatic side chains, the detachment of the aliphatic side chains and the growth of benzene rings can both increase the dipole moment, which can promote elastic modulus. In addition, the increasing number of benzene rings can create more π-π bonds between the molecules, which can lead to an increase in the intermolecular forces, further increasing the elastic modulus.
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Macromolecular Structure controlling micro mechanical properties of vitrinite and inertinite in tectonically deformed coals a case study in fengfeng coal mine of taihangshan fault zone north china
Energies, 2020Co-Authors: Anmin Wang, Daiyong Cao, Yingchun Wei, Zhifei LiuAbstract:In order to study the evolution of the mechanical properties and Macromolecular Structures in different macerals of tectonically deformed coal (TDC), vitrinite and inertinite samples were handpicked from six block TDCs in the same coal seam with an increasing deformation degree (unaltered, cataclastic, porphyroclast, scaly and powdery coal). The micro mechanical properties were tested by the nanoindentation experiment and the Macromolecular Structures were measured using 13C nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR). The results show that the range of hardness and elastic modulus of inertinite is 0.373–1.517 GPa and 4.339–12.158 GPa, respectively, which is significantly higher than that of vitrinite with values of 0.278–0.456 GPa and 4.857–7.810 GPa, respectively. From unaltered coal to powdery coal, the hardness of vitrinite and inertinite gradually decreases, with the difference between these macerals becomes smaller and the elastic modulus of vitrinite shows an increasing trend, while that of inertinite was more variable. Both the NMR and FITR results reveal that the Macromolecular Structure of inertinite has similar structural transitions as vitrinite. As the degree of deformation increases, the aliphatic side chains become shorter and the aromaticity is increasing. Macromolecular alterations caused by tectonic stress is expected to produce defects in the TDCs, therefore there should be more interspacing among the Macromolecular groups for the extrusion of macromolecules caused by the indenter of the nanoindentation experiment, thereby reducing the hardness. The elastic modulus of coal is believed to be related to intermolecular forces, which are positively correlated to the dipole moment. By calculating the dipole moments of the typical aromatic molecular Structures with aliphatic side chains, the detachment of the aliphatic side chains and the growth of benzene rings can both increase the dipole moment, which can promote elastic modulus. In addition, the increasing number of benzene rings can create more π-π bonds between the molecules, which can lead to an increase in the intermolecular forces, further increasing the elastic modulus.
