The Experts below are selected from a list of 2520 Experts worldwide ranked by ideXlab platform
Helen M Berman - One of the best experts on this subject based on the ideXlab platform.
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dnaprodb an expanded Database and web based tool for structural analysis of dna protein complexes
Nucleic Acids Research, 2019Co-Authors: Jared M Sagendorf, Helen M Berman, Nicholas Markarian, Remo RohsAbstract:DNAproDB (https://dnaprodb.usc.edu) is a web-based Database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA-protein complexes. In this paper, we report significant improvements made to DNAproDB since its initial release. DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-stranded DNA to G-quadruplexes. We have updated the structure of our data files to support complex DNA conformations, multiple DNA-protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data. Support for chemically modified residues and nucleotides has been significantly improved along with the addition of new structural features, improved structural moiety assignment and use of more sequence-based annotations. We have redesigned our report pages and search forms to support these enhancements, and the DNAproDB website has been improved to be more responsive and user-friendly. DNAproDB is now integrated with the Nucleic Acid Database, and we have increased our coverage of available Protein Data Bank entries. Our Database now contains 95% of all available DNA-protein complexes, making our tools for analysis of these structures accessible to a broad community.
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the Nucleic Acid Database new features and capabilities
Nucleic Acids Research, 2014Co-Authors: Buvaneswari Coimbatore Narayanan, John D Westbrook, Saheli Ghosh, Anton I Petrov, Blake A Sweeney, Craig L Zirbel, Neocles B Leontis, Helen M BermanAbstract:The Nucleic Acid Database (NDB) (http://ndbserver.rutgers.edu) is a web portal providing access to information about 3D Nucleic Acid structures and their complexes. In addition to primary data, the NDB contains derived geometric data, classifications of structures and motifs, standards for describing Nucleic Acid features, as well as tools and software for the analysis of Nucleic Acids. A variety of search capabilities are available, as are many different types of reports. This article describes the recent redesign of the NDB Web site with special emphasis on new RNA-derived data and annotations and their implementation and integration into the search capabilities.
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chapter 24 2 the Nucleic Acid Database
International Tables for Crystallography, 2012Co-Authors: Bohdan Schneider, Christine Zardecki, John D Westbrook, Zukang Feng, J De La Cruz, Shuchismita Dutta, Li Chen, Huanwang Yang, Jasmine Young, Helen M BermanAbstract:The Nucleic Acid Database (NDB) was one of the earliest relational Databases for use in structural biology. Today, it provides valuable resources for researchers and students. Users can search the archive using a variety of constraints, and generate quick and detailed reports. Structures can be explored through an online atlas organized by experimental and structure type. The NDB has developed and hosts standards and software tools, and offers special programs for exploring RNA structure. Keywords: Nucleic Acid Database; DNA; RNA; Nucleic Acids
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The Nucleic Acid Database
Acta Crystallographica Section B-structural Science, 2002Co-Authors: Helen M Berman, Lisa Lype, John D Westbrook, Zukang Feng, Bohdan Schneider, Christine ZardeckiAbstract:The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about Nucleic Acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for Nucleic Acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.
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The Nucleic Acid Database: A resource for Nucleic Acid science
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Helen M Berman, Christine Zardecki, John D WestbrookAbstract:The Nucleic Acid Database (NDB) distributes information about Nucleic Acid-containing structures. Here the information content of the Database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular Databases is given.
John D Westbrook - One of the best experts on this subject based on the ideXlab platform.
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the Nucleic Acid Database new features and capabilities
Nucleic Acids Research, 2014Co-Authors: Buvaneswari Coimbatore Narayanan, John D Westbrook, Saheli Ghosh, Anton I Petrov, Blake A Sweeney, Craig L Zirbel, Neocles B Leontis, Helen M BermanAbstract:The Nucleic Acid Database (NDB) (http://ndbserver.rutgers.edu) is a web portal providing access to information about 3D Nucleic Acid structures and their complexes. In addition to primary data, the NDB contains derived geometric data, classifications of structures and motifs, standards for describing Nucleic Acid features, as well as tools and software for the analysis of Nucleic Acids. A variety of search capabilities are available, as are many different types of reports. This article describes the recent redesign of the NDB Web site with special emphasis on new RNA-derived data and annotations and their implementation and integration into the search capabilities.
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chapter 24 2 the Nucleic Acid Database
International Tables for Crystallography, 2012Co-Authors: Bohdan Schneider, Christine Zardecki, John D Westbrook, Zukang Feng, J De La Cruz, Shuchismita Dutta, Li Chen, Huanwang Yang, Jasmine Young, Helen M BermanAbstract:The Nucleic Acid Database (NDB) was one of the earliest relational Databases for use in structural biology. Today, it provides valuable resources for researchers and students. Users can search the archive using a variety of constraints, and generate quick and detailed reports. Structures can be explored through an online atlas organized by experimental and structure type. The NDB has developed and hosts standards and software tools, and offers special programs for exploring RNA structure. Keywords: Nucleic Acid Database; DNA; RNA; Nucleic Acids
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The Nucleic Acid Database
Acta Crystallographica Section B-structural Science, 2002Co-Authors: Helen M Berman, Lisa Lype, John D Westbrook, Zukang Feng, Bohdan Schneider, Christine ZardeckiAbstract:The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about Nucleic Acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for Nucleic Acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.
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The Nucleic Acid Database: A resource for Nucleic Acid science
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Helen M Berman, Christine Zardecki, John D WestbrookAbstract:The Nucleic Acid Database (NDB) distributes information about Nucleic Acid-containing structures. Here the information content of the Database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular Databases is given.
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the Nucleic Acid Database present and future
Journal of Research of the National Institute of Standards and Technology, 1996Co-Authors: Helen M Berman, Christine Zardecki, Lester Clowney, A Gelbin, S H Hsieh, John D WestbrookAbstract:The Nucleic Acid Database is a relational Database containing information about three-dimensional Nucleic Acid structures. The methods used for data processing, structure validation, Database management and information retrieval, as well as the various services available via the World Wide Web, are described. Plans for the future include greater reliance on the Macromolecular Crystallographic Information File for both data processing and data management.
Remo Rohs - One of the best experts on this subject based on the ideXlab platform.
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dnaprodb an expanded Database and web based tool for structural analysis of dna protein complexes
Nucleic Acids Research, 2019Co-Authors: Jared M Sagendorf, Helen M Berman, Nicholas Markarian, Remo RohsAbstract:DNAproDB (https://dnaprodb.usc.edu) is a web-based Database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA-protein complexes. In this paper, we report significant improvements made to DNAproDB since its initial release. DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-stranded DNA to G-quadruplexes. We have updated the structure of our data files to support complex DNA conformations, multiple DNA-protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data. Support for chemically modified residues and nucleotides has been significantly improved along with the addition of new structural features, improved structural moiety assignment and use of more sequence-based annotations. We have redesigned our report pages and search forms to support these enhancements, and the DNAproDB website has been improved to be more responsive and user-friendly. DNAproDB is now integrated with the Nucleic Acid Database, and we have increased our coverage of available Protein Data Bank entries. Our Database now contains 95% of all available DNA-protein complexes, making our tools for analysis of these structures accessible to a broad community.
Christine Zardecki - One of the best experts on this subject based on the ideXlab platform.
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chapter 24 2 the Nucleic Acid Database
International Tables for Crystallography, 2012Co-Authors: Bohdan Schneider, Christine Zardecki, John D Westbrook, Zukang Feng, J De La Cruz, Shuchismita Dutta, Li Chen, Huanwang Yang, Jasmine Young, Helen M BermanAbstract:The Nucleic Acid Database (NDB) was one of the earliest relational Databases for use in structural biology. Today, it provides valuable resources for researchers and students. Users can search the archive using a variety of constraints, and generate quick and detailed reports. Structures can be explored through an online atlas organized by experimental and structure type. The NDB has developed and hosts standards and software tools, and offers special programs for exploring RNA structure. Keywords: Nucleic Acid Database; DNA; RNA; Nucleic Acids
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The Nucleic Acid Database
Acta Crystallographica Section B-structural Science, 2002Co-Authors: Helen M Berman, Lisa Lype, John D Westbrook, Zukang Feng, Bohdan Schneider, Christine ZardeckiAbstract:The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about Nucleic Acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for Nucleic Acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.
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The Nucleic Acid Database: A resource for Nucleic Acid science
Acta Crystallographica Section D-biological Crystallography, 1998Co-Authors: Helen M Berman, Christine Zardecki, John D WestbrookAbstract:The Nucleic Acid Database (NDB) distributes information about Nucleic Acid-containing structures. Here the information content of the Database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular Databases is given.
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the Nucleic Acid Database present and future
Journal of Research of the National Institute of Standards and Technology, 1996Co-Authors: Helen M Berman, Christine Zardecki, Lester Clowney, A Gelbin, S H Hsieh, John D WestbrookAbstract:The Nucleic Acid Database is a relational Database containing information about three-dimensional Nucleic Acid structures. The methods used for data processing, structure validation, Database management and information retrieval, as well as the various services available via the World Wide Web, are described. Plans for the future include greater reliance on the Macromolecular Crystallographic Information File for both data processing and data management.
Wilma K. Olson - One of the best experts on this subject based on the ideXlab platform.
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5 methylation of cytosine in cg cg base pair steps a physicochemical mechanism for the epigenetic control of dna nanomechanics
Journal of Physical Chemistry B, 2013Co-Authors: Tahir Yusufaly, Wilma K. OlsonAbstract:van der Waals density functional theory is integrated with analysis of a non-redundant set of protein–DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile “opening” mode and two shear “sliding” and “tearing” modes in the orthogonal plane. The stacking interactions of the methyl groups globally inhibit CG:CG step overtwisting while simultaneously softening the modes locally via potential energy modulations that create metastable states. Additionally, the indirect effects of the methyl groups on possible base-pair steps neighboring CG:CG are observed to be of comparable importance to their direct effects on CG:CG. The results have implications for the epigenetic control of DNA mechanics.
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geometric parameters in Nucleic Acids sugar and phosphate constituents
Journal of the American Chemical Society, 1996Co-Authors: A Gelbin, Lester Clowney, Wilma K. Olson, Bohdan Schneider, S H Hsieh, Helen M BermanAbstract:A statistical survey of the torsion angles, bond angles, and bond lengths in the sugar and phosphate groups of well-refined mononucleoside, mononucleotide, dinucleoside monophosphate, and trinucleoside diphosphate crystal structures contained in the Cambridge Structural Database and the Nucleic Acid Database is reported. The mean values of the geometrical parameters in these structures and their estimated standard deviations are separated according to their chemistry and conformation. These new parameters serve as a basis for a dictionary of standard Nucleic Acid geometry.
