910 results on '"Westbrook, John"'
Search Results
2. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.
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Vallat, Brinda, Webb, Benjamin, Westbrook, John, Goddard, Thomas, Hanke, Christian, Graziadei, Andrea, Peisach, Ezra, Zalevsky, Arthur, Sagendorf, Jared, Tangmunarunkit, Hongsuda, Voinea, Serban, Sekharan, Monica, Yu, Jian, Bonvin, Alexander, DiMaio, Frank, Hummer, Gerhard, Meiler, Jens, Tajkhorshid, Emad, Ferrin, Thomas, Lawson, Catherine, Leitner, Alexander, Rappsilber, Juri, Seidel, Claus, Jeffries, Cy, Burley, Stephen, Hoch, Jeffrey, Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, Velankar, Sameer, Schwede, Torsten, Trewhella, Jill, Kesselman, Carl, Berman, Helen, and Sali, Andrej
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Data Standard ,IHMCIF ,PDB-Dev ,PDBx/mmCIF ,Worldwide Protein Data Bank ,Databases ,Protein ,Proteins ,Protein Conformation ,Models ,Molecular ,Software ,Crystallography ,X-Ray ,Macromolecular Substances ,Computational Biology ,Ligands - Abstract
IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB.
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- 2024
3. Community recommendations on cryoEM data archiving and validation
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Kleywegt, Gerard J, Adams, Paul D, Butcher, Sarah J, Lawson, Catherine L, Rohou, Alexis, Rosenthal, Peter B, Subramaniam, Sriram, Topf, Maya, Abbott, Sanja, Baldwin, Philip R, Berrisford, John M, Bricogne, Gérard, Choudhary, Preeti, Croll, Tristan I, Danev, Radostin, Ganesan, Sai J, Grant, Timothy, Gutmanas, Aleksandras, Henderson, Richard, Heymann, J Bernard, Huiskonen, Juha T, Istrate, Andrei, Kato, Takayuki, Lander, Gabriel C, Lok, Shee-Mei, Ludtke, Steven J, Murshudov, Garib N, Pye, Ryan, Pintilie, Grigore D, Richardson, Jane S, Sachse, Carsten, Salih, Osman, Scheres, Sjors HW, Schroeder, Gunnar F, Sorzano, Carlos Oscar S, Stagg, Scott M, Wang, Zhe, Warshamanage, Rangana, Westbrook, John D, Winn, Martyn D, Young, Jasmine Y, Burley, Stephen K, Hoch, Jeffrey C, Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, and Velankar, Sameer
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Physical Sciences ,Chemical Sciences ,Physical Chemistry ,Condensed Matter Physics ,Data Curation ,Cryoelectron Microscopy ,cryogenic-specimen electron microscopy ,data archiving ,validation ,quality control ,Electron Microscopy Data Bank ,Protein Data Bank ,single-particle cryoEM ,databases ,bioinformatics ,structure determination ,Atomic ,Molecular ,Nuclear ,Particle and Plasma Physics ,Physical Chemistry (incl. Structural) ,Physical chemistry ,Condensed matter physics - Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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- 2024
4. Community recommendations on cryoEM data archiving and validation
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Kleywegt, Gerard J., Adams, Paul D., Butcher, Sarah J., Lawson, Cathy, Rohou, Alexis, Rosenthal, Peter B., Subramaniam, Sriram, Topf, Maya, Abbott, Sanja, Baldwin, Philip R., Berrisford, John M., Bricogne, Gérard, Choudhary, Preeti, Croll, Tristan I., Danev, Radostin, Ganesan, Sai J., Grant, Timothy, Gutmanas, Aleksandras, Henderson, Richard, Heymann, J. Bernard, Huiskonen, Juha T., Istrate, Andrei, Kato, Takayuki, Lander, Gabriel C., Lok, Shee-Mei, Ludtke, Steven J., Murshudov, Garib N., Pye, Ryan, Pintilie, Grigore D., Richardson, Jane S., Sachse, Carsten, Salih, Osman, Scheres, Sjors H. W., Schroeder, Gunnar F., Sorzano, Carlos Oscar S., Stagg, Scott M., Wang, Zhe, Warshamanage, Rangana, Westbrook, John D., Winn, Martyn D., Young, Jasmine Y., Burley, Stephen K., Hoch, Jeffrey C., Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, and Velankar, Sameer
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Quantitative Biology - Biomolecules - Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 45 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations., Comment: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation
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- 2023
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5. The Joneses
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Westbrook, John
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- 2018
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6. ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models
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Vallat, Brinda, Tauriello, Gerardo, Bienert, Stefan, Haas, Juergen, Webb, Benjamin M, Žídek, Augustin, Zheng, Wei, Peisach, Ezra, Piehl, Dennis W, Anischanka, Ivan, Sillitoe, Ian, Tolchard, James, Varadi, Mihaly, Baker, David, Orengo, Christine, Zhang, Yang, Hoch, Jeffrey C, Kurisu, Genji, Patwardhan, Ardan, Velankar, Sameer, Burley, Stephen K, Sali, Andrej, Schwede, Torsten, Berman, Helen M, and Westbrook, John D
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Biological Sciences ,Bioinformatics and Computational Biology ,Networking and Information Technology R&D (NITRD) ,Bioengineering ,Underpinning research ,1.4 Methodologies and measurements ,Generic health relevance ,Databases ,Protein ,Macromolecular Substances ,Protein Conformation ,Software ,ModelCIF ,PDBx/mmCIF ,Data Standard ,Computed Structure Models ,Protein Structure Prediction ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Microbiology ,Biochemistry & Molecular Biology ,Biochemistry and cell biology - Abstract
ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.
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- 2023
7. RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D
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Burley, Stephen K, Bhikadiya, Charmi, Bi, Chunxiao, Bittrich, Sebastian, Chao, Henry, Chen, Li, Craig, Paul A, Crichlow, Gregg V, Dalenberg, Kenneth, Duarte, Jose M, Dutta, Shuchismita, Fayazi, Maryam, Feng, Zukang, Flatt, Justin W, Ganesan, Sai J, Ghosh, Sutapa, Goodsell, David S, Green, Rachel Kramer, Guranovic, Vladimir, Henry, Jeremy, Hudson, Brian P, Khokhriakov, Igor, Lawson, Catherine L, Liang, Yuhe, Lowe, Robert, Peisach, Ezra, Persikova, Irina, Piehl, Dennis W, Rose, Yana, Sali, Andrej, Segura, Joan, Sekharan, Monica, Shao, Chenghua, Vallat, Brinda, Voigt, Maria, Webb, Benjamin, Westbrook, John D, Whetstone, Shamara, Young, Jasmine Y, Zalevsky, Arthur, and Zardecki, Christine
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Biochemistry and Cell Biology ,Biological Sciences ,Bioengineering ,Humans ,Protein Conformation ,Databases ,Protein ,Proteins ,Computational Biology ,Macromolecular Substances ,electron microscopy ,macromolecular crystallography ,micro-electron diffraction ,Mol* ,nuclear magnetic resonance spectroscopy ,open access ,PDB ,Protein Data Bank ,RCSB Protein Data Bank ,Worldwide Protein Data Bank ,Computation Theory and Mathematics ,Other Information and Computing Sciences ,Biophysics ,Biochemistry and cell biology ,Medicinal and biomolecular chemistry - Abstract
Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open-access global archive housing three-dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB-designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction). The RCSB PDB research-focused web portal (RCSB.org) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal (PDB101.RCSB.org) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB-designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org; and (v) supports training, outreach, and education via PDB101.RCSB.org. New tools and features at RCSB.org are presented using examples drawn from high-resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.
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- 2022
8. Contributors
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Barber, Jesse R., primary, Becker, Daniel J., additional, Boyles, Justin G., additional, Clare, Elizabeth L., additional, Conenna, Irene, additional, Currie, Shannon E., additional, de Wit, Luz A., additional, Dechmann, Dina K.N., additional, Denzinger, Annette, additional, Diebold, Clarice Anna, additional, Fenton, Brock, additional, Frick, Winifred F., additional, Ibarra, Ana, additional, Ingala, Melissa R., additional, Jones, Matthew F., additional, Kohles, Jenna E., additional, Korine, Carmi, additional, Krauel, Jennifer J., additional, Lear, Kristen, additional, Lučan, Radek K., additional, McCracken, Gary F., additional, McGuire, Liam P., additional, Mikula, Peter, additional, Moss, Cynthia F., additional, Muchhala, Nathan, additional, Oelbaum, Phillip J., additional, O’Mara, M. Teague, additional, Pellón, Juan J., additional, Ratcliffe, John M., additional, Reynolds, Don R., additional, Russo, Danilo, additional, Sánchez, Cecilia A., additional, Sandoval-Herrera, Natalia I., additional, Schnitzler, Hans-Ulrich, additional, Simmons, Nancy B., additional, Simonis, Molly C., additional, Valdez, Jose W., additional, Voigt, Christian C., additional, Westbrook, John K., additional, and Yu, Rieka, additional
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- 2024
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9. PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.
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Westbrook, John D, Young, Jasmine Y, Shao, Chenghua, Feng, Zukang, Guranovic, Vladimir, Lawson, Catherine L, Vallat, Brinda, Adams, Paul D, Berrisford, John M, Bricogne, Gerard, Diederichs, Kay, Joosten, Robbie P, Keller, Peter, Moriarty, Nigel W, Sobolev, Oleg V, Velankar, Sameer, Vonrhein, Clemens, Waterman, David G, Kurisu, Genji, Berman, Helen M, Burley, Stephen K, and Peisach, Ezra
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Macromolecular Substances ,Crystallography ,Computational Biology ,Molecular Biology ,Protein Conformation ,Semantics ,Software ,Databases ,Protein ,biological data ,data management ,data standard ,macromolecular structure ,protein data bank ,Bioengineering ,Networking and Information Technology R&D (NITRD) ,1.5 Resources and infrastructure (underpinning) ,Underpinning research ,Generic health relevance ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Microbiology ,Biochemistry & Molecular Biology - Abstract
PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.
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- 2022
10. Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank
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Baskaran, Kumaran, Ploskon, Eliza, Tejero, Roberto, Yokochi, Masashi, Harrus, Deborah, Liang, Yuhe, Peisach, Ezra, Persikova, Irina, Ramelot, Theresa A., Sekharan, Monica, Tolchard, James, Westbrook, John D., Bardiaux, Benjamin, Schwieters, Charles D., Patwardhan, Ardan, Velankar, Sameer, Burley, Stephen K., Kurisu, Genji, Hoch, Jeffrey C., Montelione, Gaetano T., Vuister, Geerten W., and Young, Jasmine Y.
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- 2024
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11. New system for archiving integrative structures
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Vallat, Brinda, Webb, Benjamin, Fayazi, Maryam, Voinea, Serban, Tangmunarunkit, Hongsuda, Ganesan, Sai J, Lawson, Catherine L, Westbrook, John D, Kesselman, Carl, Sali, Andrej, and Berman, Helen M
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Databases ,Protein ,Information Storage and Retrieval ,Protein Conformation ,Proteins ,PDB-Dev ,integrative modeling ,PDBx/mmCIF ,IHM-dictionary ,data standards ,Physical Sciences ,Chemical Sciences ,Biological Sciences ,Biophysics - Abstract
Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined. A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, PDB-Dev ensures that the results of integrative structure determinations are freely accessible to everyone.
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- 2021
12. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
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Burley, Stephen K., Berman, Helen M., Chiu, Wah, Dai, Wei, Flatt, Justin W., Hudson, Brian P., Kaelber, Jason T., Khare, Sagar D., Kulczyk, Arkadiusz W., Lawson, Catherine L., Pintilie, Grigore D., Sali, Andrej, Vallat, Brinda, Westbrook, John D., Young, Jasmine Y., and Zardecki, Christine
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- 2022
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13. RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances
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Bittrich, Sebastian, Bhikadiya, Charmi, Bi, Chunxiao, Chao, Henry, Duarte, Jose M., Dutta, Shuchismita, Fayazi, Maryam, Henry, Jeremy, Khokhriakov, Igor, Lowe, Robert, Piehl, Dennis W., Segura, Joan, Vallat, Brinda, Voigt, Maria, Westbrook, John D., Burley, Stephen K., and Rose, Yana
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- 2023
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14. The TRUST Principles for digital repositories.
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Lin, Dawei, Crabtree, Jonathan, Dillo, Ingrid, Downs, Robert R, Edmunds, Rorie, Giaretta, David, De Giusti, Marisa, L'Hours, Hervé, Hugo, Wim, Jenkyns, Reyna, Khodiyar, Varsha, Martone, Maryann E, Mokrane, Mustapha, Navale, Vivek, Petters, Jonathan, Sierman, Barbara, Sokolova, Dina V, Stockhause, Martina, and Westbrook, John
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- 2020
15. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
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Berman, Helen M, Adams, Paul D, Bonvin, Alexandre A, Burley, Stephen K, Carragher, Bridget, Chiu, Wah, DiMaio, Frank, Ferrin, Thomas E, Gabanyi, Margaret J, Goddard, Thomas D, Griffin, Patrick R, Haas, Juergen, Hanke, Christian A, Hoch, Jeffrey C, Hummer, Gerhard, Kurisu, Genji, Lawson, Catherine L, Leitner, Alexander, Markley, John L, Meiler, Jens, Montelione, Gaetano T, Phillips, George N, Prisner, Thomas, Rappsilber, Juri, Schriemer, David C, Schwede, Torsten, Seidel, Claus AM, Strutzenberg, Timothy S, Svergun, Dmitri I, Tajkhorshid, Emad, Trewhella, Jill, Vallat, Brinda, Velankar, Sameer, Vuister, Geerten W, Webb, Benjamin, Westbrook, John D, White, Kate L, and Sali, Andrej
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Biological Sciences ,Computational Biology ,Crystallography ,X-Ray ,Databases ,Protein ,Magnetic Resonance Spectroscopy ,Models ,Molecular ,Protein Conformation ,Proteins ,Biophysics - Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.
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- 2019
16. Interventions for Improving Employment Outcomes for Persons with Autism Spectrum Disorders: A Systematic Review Update
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Fong, Carlton J., Taylor, Joshua, Berdyyeva, Aynura, McClelland, Amanda M., Murphy, Kathleen M., and Westbrook, John D.
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The objective of this review is to determine the effectiveness of employment interventions in securing and maintaining employment for adults and transition-age youth with autism spectrum disorders (ASD), updating two reviews by Westbrook et al. (2012a, 2013). The comprehensive search strategy used to identify relevant studies included a review of 28 relevant electronic databases. Selection criteria consisted of an intervention evaluation using a randomized controlled trial or quasi-experimental design, an employment outcome, and a population of individuals with ASD. The systematic review update identified three studies that evaluated employment outcomes for interventions for individuals with ASD. All three studies identified in the review suggest that vocation-focused programs may have positive impacts on the employment outcomes for individuals with ASD. Given that prior reviews did not identify interventions with actual employment outcomes, the more recent emergence of evaluations of such programs is encouraging. This suggests that there is a growing body of evidence regarding interventions to enhance the employment outcomes for individuals with ASD but also greater need to conduct rigorous trials of vocation-based interventions for individuals with ASD that measure employment outcomes.
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- 2021
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17. Archiving and disseminating integrative structure models.
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Vallat, Brinda, Webb, Benjamin, Westbrook, John, Sali, Andrej, and Berman, Helen M
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Proteins ,Molecular Conformation ,Protein Conformation ,Models ,Molecular ,Software ,Workflow ,Deposition ,Hybrid modeling ,Integrative modeling ,Model validation ,PDB ,mmCIF dictionary ,Models ,Molecular ,Physical Sciences ,Chemical Sciences ,Biological Sciences ,Biophysics - Abstract
Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format.
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- 2019
18. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)
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Adams, Paul D, Afonine, Pavel V, Baskaran, Kumaran, Berman, Helen M, Berrisford, John, Bricogne, Gerard, Brown, David G, Burley, Stephen K, Chen, Minyu, Feng, Zukang, Flensburg, Claus, Gutmanas, Aleksandras, Hoch, Jeffrey C, Ikegawa, Yasuyo, Kengaku, Yumiko, Krissinel, Eugene, Kurisu, Genji, Liang, Yuhe, Liebschner, Dorothee, Mak, Lora, Markley, John L, Moriarty, Nigel W, Murshudov, Garib N, Noble, Martin, Peisach, Ezra, Persikova, Irina, Poon, Billy K, Sobolev, Oleg V, Ulrich, Eldon L, Velankar, Sameer, Vonrhein, Clemens, Westbrook, John, Wojdyr, Marcin, Yokochi, Masashi, and Young, Jasmine Y
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Biochemistry and Cell Biology ,Biological Sciences ,Crystallography ,X-Ray ,Database Management Systems ,Databases ,Protein ,Humans ,Protein Conformation ,Proteins ,Software ,PDB ,mmCIF ,OneDep ,wwPDB ,data dictionary ,data archiving ,biocuration ,validation ,macromolecular crystallography ,data standards ,PDBx ,mmCIF format ,Protein Data Bank ,Worldwide Protein Data Bank ,PDBx/mmCIF format ,Physical Sciences ,Chemical Sciences ,Biophysics ,Biological sciences ,Chemical sciences ,Physical sciences - Abstract
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
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- 2019
19. RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
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Burley, Stephen K, Berman, Helen M, Bhikadiya, Charmi, Bi, Chunxiao, Chen, Li, Di Costanzo, Luigi, Christie, Cole, Dalenberg, Ken, Duarte, Jose M, Dutta, Shuchismita, Feng, Zukang, Ghosh, Sutapa, Goodsell, David S, Green, Rachel K, Guranović, Vladimir, Guzenko, Dmytro, Hudson, Brian P, Kalro, Tara, Liang, Yuhe, Lowe, Robert, Namkoong, Harry, Peisach, Ezra, Periskova, Irina, Prlić, Andreas, Randle, Chris, Rose, Alexander, Rose, Peter, Sala, Raul, Sekharan, Monica, Shao, Chenghua, Tan, Lihua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John, Woo, Jesse, Yang, Huanwang, Young, Jasmine, Zhuravleva, Marina, and Zardecki, Christine
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Biomedical Research ,Biotechnology ,Data Curation ,Databases ,Protein ,Protein Conformation ,Software ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'
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- 2019
20. Areawide management of fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), using selected cover crop plants
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Meagher, Jr., Robert L., Nagoshi, Rodney N., Fleischer, Shelby J., Westbrook, John K., Wright, David L., Morris, J. Bradley, Brown, James T., and Rowley, Amy J.
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- 2022
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21. Comparison of bee composition in sunn hemp and other cover crops
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Meagher, Robert L., Watrous, Kristal M., Fleischer, Shelby J., Nagoshi, Rodney N., Brown, James T., and Westbrook, John K.
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- 2020
22. Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules
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Vallat, Brinda, Webb, Benjamin, Westbrook, John D, Sali, Andrej, and Berman, Helen M
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Biochemistry and Cell Biology ,Biological Sciences ,Bioengineering ,Databases ,Protein ,Internet ,Macromolecular Substances ,Models ,Molecular ,Protein Conformation ,Proteins ,IHM dictionary ,PDB ,PDB-Dev ,PDBx/mmCIF ,data archiving ,data standards ,integrative/hybrid modeling ,multi-scale models ,spatial restraints ,structural biology ,Chemical Sciences ,Information and Computing Sciences ,Biophysics ,Biological sciences ,Chemical sciences - Abstract
Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions.
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- 2018
23. Community recommendations on cryoEM data archiving and validation
- Author
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Kleywegt, Gerard J., primary, Adams, Paul D., additional, Butcher, Sarah J., additional, Lawson, Catherine L., additional, Rohou, Alexis, additional, Rosenthal, Peter B., additional, Subramaniam, Sriram, additional, Topf, Maya, additional, Abbott, Sanja, additional, Baldwin, Philip R., additional, Berrisford, John M., additional, Bricogne, Gérard, additional, Choudhary, Preeti, additional, Croll, Tristan I., additional, Danev, Radostin, additional, Ganesan, Sai J., additional, Grant, Timothy, additional, Gutmanas, Aleksandras, additional, Henderson, Richard, additional, Heymann, J. Bernard, additional, Huiskonen, Juha T., additional, Istrate, Andrei, additional, Kato, Takayuki, additional, Lander, Gabriel C., additional, Lok, Shee-Mei, additional, Ludtke, Steven J., additional, Murshudov, Garib N., additional, Pye, Ryan, additional, Pintilie, Grigore D., additional, Richardson, Jane S., additional, Sachse, Carsten, additional, Salih, Osman, additional, Scheres, Sjors H. W., additional, Schroeder, Gunnar F., additional, Sorzano, Carlos Oscar S., additional, Stagg, Scott M., additional, Wang, Zhe, additional, Warshamanage, Rangana, additional, Westbrook, John D., additional, Winn, Martyn D., additional, Young, Jasmine Y., additional, Burley, Stephen K., additional, Hoch, Jeffrey C., additional, Kurisu, Genji, additional, Morris, Kyle, additional, Patwardhan, Ardan, additional, and Velankar, Sameer, additional
- Published
- 2024
- Full Text
- View/download PDF
24. Behavioral, Psychological, Educational, and Vocational Interventions to Facilitate Employment Outcomes for Cancer Survivors: A Systematic Review. Campbell Systematic Reviews 2015:5
- Author
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Campbell Collaboration, Fong, Carlton J., Murphy, Kathleen M., Westbrook, John D., and Markle, Minda M.
- Abstract
In the United States, an estimated 1.5 million people are diagnosed annually with some type of cancer (American Cancer Society, 2011). Work is an important stabilizing factor for cancer survivors (Arnold, 1999). De Boer and colleagues (2009) identified a rate of 33.8% unemployment among cancer survivors beyond the age of 18 compared to 15.2% among a healthy international control population. Greater awareness of the job-related and workplace issues that cancer survivors face can lead to more comprehensive rehabilitation plans and recovery (Centers for Disease Control, 2011; Nathan, Hayes-Lattin, Sisler, & Hudson, 2011). Although various recent interventions have been developed to address unemployment among cancer survivors, these have not yet been systematically evaluated. The objective of this systematic review is to examine experimental and quasi-experimental studies about interventions that (i) include one or more behavioral, psychological, educational, or vocational components, (ii) involve cancer survivors aged 18 years or older, and (iii) assess intervention outcomes on employment outcomes. The aims are both to describe the variety of interventions that have been studied using rigorous methods and to estimate intervention effects. This review highlights the positive effect psychosocial interventions may have on employment outcomes for cancer survivors. However, the methodological shortcomings of the included studies overall makes it likely that there is bias in the results and too few studies to provide sufficiently strong evidence to recommend particular practices. This review brings attention to the need for additional rigorous studies in this area, in particular, randomized controlled trials with more detailed reporting of data and study design and methodology. Appended are: (1) Documentation of Search Strategies for the Systematic Review; (2) Coding Form; and (3) Reasons Stage 2 Studies Were Excluded from the Systematic Review.
- Published
- 2015
25. Modeling the dispersal of wind-borne pests: Sensitivity of infestation forecasts to uncertainty in parameterization of long-distance airborne dispersal
- Author
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Koralewski, Tomasz E., Wang, Hsiao-Hsuan, Grant, William E., Brewer, Michael J., Elliott, Norman C., and Westbrook, John K.
- Published
- 2021
- Full Text
- View/download PDF
26. The RCSB protein data bank: integrative view of protein, gene and 3D structural information
- Author
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Rose, Peter W, Prlić, Andreas, Altunkaya, Ali, Bi, Chunxiao, Bradley, Anthony R, Christie, Cole H, Di Costanzo, Luigi, Duarte, Jose M, Dutta, Shuchismita, Feng, Zukang, Green, Rachel Kramer, Goodsell, David S, Hudson, Brian, Kalro, Tara, Lowe, Robert, Peisach, Ezra, Randle, Christopher, Rose, Alexander S, Shao, Chenghua, Tao, Yi-Ping, Valasatava, Yana, Voigt, Maria, Westbrook, John D, Woo, Jesse, Yang, Huangwang, Young, Jasmine Y, Zardecki, Christine, Berman, Helen M, and Burley, Stephen K
- Subjects
Bioengineering ,1.5 Resources and infrastructure (underpinning) ,Underpinning research ,Generic health relevance ,Computational Biology ,Databases ,Genetic ,Datasets as Topic ,Metabolic Networks and Pathways ,Models ,Molecular ,Protein Conformation ,Proteins ,Software ,Structure-Activity Relationship ,User-Computer Interface ,Web Browser ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive.
- Published
- 2017
27. Community recommendations on cryoEM data archiving and validation
- Author
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Wellcome Trust, National Science Foundation (US), Department of Energy (US), National Cancer Institute (US), National Institute of Allergy and Infectious Diseases (US), National Institutes of Health (US), National Institute of General Medical Sciences (US), Kleywegt, Gerard J., Adams, Paul D., Butcher, Sarah J., Lawson, Catherine L., Rohou, Alexis, Rosenthal, Peter B., Subramaniam, Sriram, Topf, Maya, Abbott, Sanja, Baldwin, Philip R., Berrisford, John M., Bricogne, Gérard, Choudhary, Preeti, Croll, Tristan I., Danev, Radostin, Ganesan, Sai J., Grant, Timothy, Gutmanas, Aleksandras, Henderson, Richard, Heymann, J. Bernard, Huiskonen, Juha T., Istrate, Andrei, Kato, Takayuki, Lander, Gabriel C., Lok, Shee-Mei, Ludtke, Steven J., Murshudov, Garib N., Pye, Ryan, Pintilie, Grigore D., Richardson, Jane S., Sachse, Carsten, Salih, Osman, Scheres, Sjors H. W., Schroeder, Gunnar F., Sorzano, Carlos Óscar S., Stagg, Scott M., Wang, Zhe, Warshamanage, Rangana, Westbrook, John D., Winn, Martyn D., Young, Jasmine Y., Burley, Stephen K., Hoch, Jeffrey C., Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, Velankar, Sameer, Wellcome Trust, National Science Foundation (US), Department of Energy (US), National Cancer Institute (US), National Institute of Allergy and Infectious Diseases (US), National Institutes of Health (US), National Institute of General Medical Sciences (US), Kleywegt, Gerard J., Adams, Paul D., Butcher, Sarah J., Lawson, Catherine L., Rohou, Alexis, Rosenthal, Peter B., Subramaniam, Sriram, Topf, Maya, Abbott, Sanja, Baldwin, Philip R., Berrisford, John M., Bricogne, Gérard, Choudhary, Preeti, Croll, Tristan I., Danev, Radostin, Ganesan, Sai J., Grant, Timothy, Gutmanas, Aleksandras, Henderson, Richard, Heymann, J. Bernard, Huiskonen, Juha T., Istrate, Andrei, Kato, Takayuki, Lander, Gabriel C., Lok, Shee-Mei, Ludtke, Steven J., Murshudov, Garib N., Pye, Ryan, Pintilie, Grigore D., Richardson, Jane S., Sachse, Carsten, Salih, Osman, Scheres, Sjors H. W., Schroeder, Gunnar F., Sorzano, Carlos Óscar S., Stagg, Scott M., Wang, Zhe, Warshamanage, Rangana, Westbrook, John D., Winn, Martyn D., Young, Jasmine Y., Burley, Stephen K., Hoch, Jeffrey C., Kurisu, Genji, Morris, Kyle, Patwardhan, Ardan, and Velankar, Sameer
- Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop’s motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
- Published
- 2024
28. Impact of the Protein Data Bank on antineoplastic approvals
- Author
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Westbrook, John D., Soskind, Rose, Hudson, Brian P., and Burley, Stephen K.
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- 2020
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29. Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank
- Author
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Baskaran, Kumaran, primary, Ploskon, Eliza, additional, Tejero, Roberto, additional, Yokochi, Masashi, additional, Harrus, Deborah, additional, Liang, Yuhe, additional, Peisach, Ezra, additional, Persikova, Irina, additional, Ramelot, Theresa A., additional, Sekharan, Monica, additional, Tolchard, James, additional, Westbrook, John D., additional, Bardiaux, Benjamin, additional, Schwieters, Charles D., additional, Patwardhan, Ardan, additional, Velankar, Sameer, additional, Burley, Stephen K., additional, Kurisu, Genji, additional, Hoch, Jeffrey C., additional, Montelione, Gaetano T., additional, Vuister, Geerten W., additional, and Young, Jasmine Y., additional
- Published
- 2024
- Full Text
- View/download PDF
30. PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
- Author
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Choudhary, Preeti, primary, Feng, Zukang, additional, Berrisford, John, additional, Chao, Henry, additional, Ikegawa, Yasuyo, additional, Peisach, Ezra, additional, Piehl, Dennis W, additional, Smith, James, additional, Tanweer, Ahsan, additional, Varadi, Mihaly, additional, Westbrook, John D, additional, Young, Jasmine Y, additional, Patwardhan, Ardan, additional, Morris, Kyle L, additional, Hoch, Jeffrey C, additional, Kurisu, Genji, additional, Velankar, Sameer, additional, and Burley, Stephen K, additional
- Published
- 2024
- Full Text
- View/download PDF
31. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
- Author
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Adams, Paul D, Aertgeerts, Kathleen, Bauer, Cary, Bell, Jeffrey A, Berman, Helen M, Bhat, Talapady N, Blaney, Jeff M, Bolton, Evan, Bricogne, Gerard, Brown, David, Burley, Stephen K, Case, David A, Clark, Kirk L, Darden, Tom, Emsley, Paul, Feher, Victoria A, Feng, Zukang, Groom, Colin R, Harris, Seth F, Hendle, Jorg, Holder, Thomas, Joachimiak, Andrzej, Kleywegt, Gerard J, Krojer, Tobias, Marcotrigiano, Joseph, Mark, Alan E, Markley, John L, Miller, Matthew, Minor, Wladek, Montelione, Gaetano T, Murshudov, Garib, Nakagawa, Atsushi, Nakamura, Haruki, Nicholls, Anthony, Nicklaus, Marc, Nolte, Robert T, Padyana, Anil K, Peishoff, Catherine E, Pieniazek, Susan, Read, Randy J, Shao, Chenghua, Sheriff, Steven, Smart, Oliver, Soisson, Stephen, Spurlino, John, Stouch, Terry, Svobodova, Radka, Tempel, Wolfram, Terwilliger, Thomas C, Tronrud, Dale, Velankar, Sameer, Ward, Suzanna C, Warren, Gregory L, Westbrook, John D, Williams, Pamela, Yang, Huanwang, and Young, Jasmine
- Subjects
Generic health relevance ,Crystallography ,X-Ray ,Data Curation ,Databases ,Protein ,Guidelines as Topic ,Ligands ,Models ,Molecular ,Protein Conformation ,Proteins ,Biophysics - Abstract
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
- Published
- 2016
32. Pre-Graduation Transition Services for Improving Employment Outcomes among Persons with Autism Spectrum Disorders: A Systematic Review. Campbell Systematic Reviews 2013:11
- Author
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Campbell Collaboration, Westbrook, John D., Fong, Carlton J., and Nye, Chad
- Abstract
Background: As the number of individuals diagnosed with autism spectrum disorders (ASD) rises, attention is increasingly focused on potential employment outcomes for individuals with ASD, especially for those individuals that are exiting public school settings. Individuals without disabilities are eight times more likely to be employed than individuals with severe disabilities (National Organization on Disability, 2000). Individuals with ASD are among those least likely to be employed (Cameto, Marder, Wagner, & Cardoso, 2003; Dew & Alan, 2007). Although economic conditions and employer attitudes are important factors in acquiring employment opportunities for individuals with ASD, appropriately addressing specific behaviors common among individuals with ASD can greatly improve employment outcomes (Schaller & Yang, 2005). Objective: To determine the effectiveness of pre-graduation interventions aimed at persons with autism spectrum disorders to shape behaviors, social interactions, and/or skills that result in employment in mainstream competitive employment settings. Search Strategy: Studies were identified using electronic search techniques of 30 computerized databases. The keywords used in the computerized bibliography searches were divided into three categories: population, treatment, and domain and design characteristics. The searches covered the period from 1943 through 2011. Grey literature identified through electronic searches was submitted to the same inclusion criteria as other studies. The same time range (1943-2011) and inclusion criteria were applied to a search of the grey literature for unpublished studies. References from individual studies were searched for potential studies to consider for inclusion. In addition, unpublished dissertations and theses were identified through the search strategy for review and consideration. A two-stage process was used to determine inclusion or exclusion of studies: (1) title and abstract stage and (2) full text stage. The participant sample of the study was secondary school-age individuals (ages 14-22), with a diagnosis of Autism Spectrum Disorder (ASD). Interventions for this review were included if they were designed as an approach to prepare and/or place transition-age individuals with ASD into gainful employment. Interventions that address the acquisition of job-related skills/behaviors or social employment-appropriate skills/behaviors without an employment outcome were excluded. Studies with a research design of randomized controlled trials, quasi-experimental, or single subject experimental were coded for inclusion. Data Collection & Analysis: The combined electronic and hand searches produced a total of 5,665 citations at Stage 1 Title/Abstract. Of these studies a total of 85 citations were advanced for collection of a full text copy of the study (Full-Text Stage 2). The search results were examined independently by three of the review authors. Results: This review was not able to identify definitive interventions that predictably and positively supported the development of transition programs designed to produce employment outcomes for individuals with ASD. Upon review of the full-text for each of the 85 studies, no studies were identified that met all the inclusion criteria specified for the review. The following describes the reasons for exclusion of the studies identified through the Stage 2 review procedures: studies that did not describe or assess an intervention (n = 40), did not present outcomes related with gainful employment (n = 38), did not contain participants with ASD (n = 3), or did not provide quantitative data (case study) (n = 4). Authors' Conclusions: While no definitive conclusions can be drawn based upon the current review, the authors did identify qualitative research and other related studies that addressed elements of potential successful employment placements for transition-age individuals with ASD that are detailed in Appendix B. Given the regulations and funding often surrounding transition programming for students with disabilities, it is remarkable that such limited research attention has been paid to the effectiveness of interventions that produce the intended result of such programs. Future research efforts are needed to develop studies that utilize a rigorous experimental design to determine the relative effectiveness of the various interventions being utilized in transition programming for students with ASD. It is also important for such studies to identify actual employment outcomes that result from presumed preparatory or facilitating interventions utilized in transition programs. The following are appended: (1) Glossary of Job Support and Intervention Terminology; (2) A Nonsystematic Review of Selected, Excluded Studies 34 (a) 8.2.1 Implications Of Associated Qualitative Research and Other Related Studies; and (b) 8.2.2 Characteristics of Discussion Studies Cited; (3) Documentation of search strategies for the systematic review; (4) Coding form: employment for individuals with autism studies; (5) Reasons stage 2 studies were excluded from the systematic review; and (6) References to studies excluded from the systematic review. [This systematic review was funded by the Education Coordinating Group of the Campbell Collaboration.]
- Published
- 2013
33. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
- Author
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Sali, Andrej, Berman, Helen M, Schwede, Torsten, Trewhella, Jill, Kleywegt, Gerard, Burley, Stephen K, Markley, John, Nakamura, Haruki, Adams, Paul, Bonvin, Alexandre MJJ, Chiu, Wah, Peraro, Matteo Dal, Di Maio, Frank, Ferrin, Thomas E, Grünewald, Kay, Gutmanas, Aleksandras, Henderson, Richard, Hummer, Gerhard, Iwasaki, Kenji, Johnson, Graham, Lawson, Catherine L, Meiler, Jens, Marti-Renom, Marc A, Montelione, Gaetano T, Nilges, Michael, Nussinov, Ruth, Patwardhan, Ardan, Rappsilber, Juri, Read, Randy J, Saibil, Helen, Schröder, Gunnar F, Schwieters, Charles D, Seidel, Claus AM, Svergun, Dmitri, Topf, Maya, Ulrich, Eldon L, Velankar, Sameer, and Westbrook, John D
- Subjects
Humans ,Proteins ,Computational Biology ,Protein Conformation ,Models ,Molecular ,Databases ,Protein ,Advisory Committees ,Chemical Sciences ,Biological Sciences ,Information and Computing Sciences ,Biophysics - Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?
- Published
- 2015
34. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
- Author
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Rose, Peter W, Prlić, Andreas, Bi, Chunxiao, Bluhm, Wolfgang F, Christie, Cole H, Dutta, Shuchismita, Green, Rachel Kramer, Goodsell, David S, Westbrook, John D, Woo, Jesse, Young, Jasmine, Zardecki, Christine, Berman, Helen M, Bourne, Philip E, and Burley, Stephen K
- Subjects
Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Biological Sciences ,Bioengineering ,Networking and Information Technology R&D (NITRD) ,1.5 Resources and infrastructure (underpinning) ,Underpinning research ,Generic health relevance ,Binding Sites ,Databases ,Protein ,Internet ,Membrane Proteins ,Molecular Biology ,Molecular Sequence Annotation ,Multiprotein Complexes ,Peptides ,Pharmaceutical Preparations ,Protein Conformation ,Research ,Software ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.
- Published
- 2015
35. The Challenge of Evidence in Disability and Rehabilitation Research and Practice: A Position Paper
- Author
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SEDL, National Center for the Dissemination of Disability Research (NCDDR), Johnston, Mark V., Vanderheiden, Gregg C., Farkas, Marianne D., Rogers, E. Sally, Summers, Jean Ann, and Westbrook, John D.
- Abstract
This paper states the position of the National Center for the Dissemination of Disability Research (NCDDR) Task Force on Standards of Evidence and Methods (TFSE) regarding the need for (a) the thoughtful determination of research evidence on the basis of both the rigor of the research and the relevance of the research to the lives of people with disabilities; and (b) systems that facilitate our ability, on a timely basis, to describe what the best available evidence is in response to specific topical questions in disability and rehabilitation. The primary focus of this paper is on evidence for interventions in the field of disability and rehabilitation (D&R). Evidence issues related to D&R interventions concern all people with disabilities and involve both research and development, as both are extremely important. The specific objectives of this paper are the following: (1) To clarify what is meant by the term evidence and to describe the nature of the contemporary systems used to identify and evaluate evidence in intervention research; (2) To identify the challenges in meeting contemporary standards of evidence in the field of D&R interventions; and (3) To propose next steps for examining related issues and for taking action to promote the availability of evidence-based services and information in the field of D&R interventions. [This paper was developed as a group effort of the National Center for the Dissemination of Disability Research (NCDDR) Task Force on Standards of Evidence and Methods (TFSE).]
- Published
- 2009
36. Archiving of Integrative Structural Models
- Author
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Berman, Helen M., Trewhella, Jill, Vallat, Brinda, Westbrook, John D., COHEN, IRUN R., Series Editor, LAJTHA, ABEL, Series Editor, LAMBRIS, JOHN D., Series Editor, PAOLETTI, RODOLFO, Series Editor, Rezaei, Nima, Series Editor, Nakamura, Haruki, editor, Kleywegt, Gerard, editor, Burley, Stephen K., editor, and Markley, John L., editor
- Published
- 2018
- Full Text
- View/download PDF
37. Psychological Interventions to Facilitate Employment Outcomes for Cancer Survivors: A Systematic Review and Meta-Analysis
- Author
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Fong, Carlton J., Murphy, Kathleen M., Westbrook, John D., and Markle, Minda M.
- Abstract
Purpose: The objective was to examine experimental and quasi-experimental studies about interventions that (i) included behavioral, psychological, educational, or vocational components; (ii) involved cancer survivors aged 18 years or older; and (iii) assessed employment outcomes. Methods: The aims were both to describe the variety of interventions that have been studied using rigorous methods and to estimate intervention effects using systematic review and meta-analysis methodologies. Results: We found 12 studies evaluating the effects of psychosocial interventions on the employment of cancer survivors (N = 2,151). Overall, there were positive effects on employment status but no evidence of an effect on hours worked and sick leave. Discussion: Despite the positive effect of psychosocial interventions, methodological shortcomings of the included studies overall make it likely that there was bias in the results and too few studies to provide sufficient evidence to recommend particular practices. This review brings attention to the need for additional rigorous studies.
- Published
- 2018
- Full Text
- View/download PDF
38. PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank
- Author
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Choudhary, Preeti, primary, Feng, Zukang, additional, Berrisford, John, additional, Chao, Henry, additional, Ikegawa, Yasuyo, additional, Peisach, Ezra, additional, Piehl, Dennis W., additional, Smith, James, additional, Tanweer, Ahsan, additional, Varadi, Mihaly, additional, Westbrook, John D., additional, Young, Jasmine Y., additional, Patwardhan, Ardan, additional, Morris, Kyle L., additional, Hoch, Jeffrey C., additional, Kurisu, Genji, additional, Velankar, Sameer, additional, and Burley, Stephen K., additional
- Published
- 2023
- Full Text
- View/download PDF
39. PDB-Dev: a prototype system for archiving integrative structures
- Author
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Vallat, Brinda, primary, Webb, Benjamin, additional, Zalevsky, Arthur, additional, Voinea, Serban, additional, Tangmunarunkit, Hongsuda, additional, Sekharan, Monica, additional, Westbrook, John D., additional, Kesselman, Carl, additional, Burley, Stephen K., additional, Berman, Helen M., additional, and Sali, Andrej, additional
- Published
- 2023
- Full Text
- View/download PDF
40. Predator–prey interaction reveals local effects of high-altitude insect migration
- Author
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Krauel, Jennifer J., Brown, Veronica A., Westbrook, John K., and McCracken, Gary F.
- Published
- 2018
41. The RCSB Protein Data Bank: new resources for research and education
- Author
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Rose, Peter W, Bi, Chunxiao, Bluhm, Wolfgang F, Christie, Cole H, Dimitropoulos, Dimitris, Dutta, Shuchismita, Green, Rachel K, Goodsell, David S, Prlić, Andreas, Quesada, Martha, Quinn, Gregory B, Ramos, Alexander G, Westbrook, John D, Young, Jasmine, Zardecki, Christine, Berman, Helen M, and Bourne, Philip E
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Generic health relevance ,Biochemistry ,Computer Graphics ,Databases ,Protein ,Internet ,Ligands ,Protein Conformation ,Protein Structure ,Tertiary ,Research ,Structural Homology ,Protein ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) develops tools and resources that provide a structural view of biology for research and education. The RCSB PDB web site (http://www.rcsb.org) uses the curated 3D macromolecular data contained in the PDB archive to offer unique methods to access, report and visualize data. Recent activities have focused on improving methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments. New educational resources are offered at the PDB-101 educational view of the main web site such as Author Profiles that display a researcher's PDB entries in a timeline. To promote different kinds of access to the RCSB PDB, Web Services have been expanded, and an RCSB PDB Mobile application for the iPhone/iPad has been released. These improvements enable new opportunities for analyzing and understanding structure data.
- Published
- 2013
42. Economic Value of the Pest Control Service Provided by Brazilian Free-Tailed Bats in South-Central Texas
- Author
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Cleveland, Cutler J., Betke, Margrit, Federico, Paula, Frank, Jeff D., Hallam, Thomas G., Horn, Jason, López, Juan D., McCracken, Gary F., Medellín, Rodrigo A., Moreno-Valdez, Arnulfo, Sansone, Chris G., Westbrook, John K., and Kunz, Thomas H.
- Published
- 2006
43. The RCSB Protein Data Bank: redesigned web site and web services
- Author
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Rose, Peter W, Beran, Bojan, Bi, Chunxiao, Bluhm, Wolfgang F, Dimitropoulos, Dimitris, Goodsell, David S, Prlić, Andreas, Quesada, Martha, Quinn, Gregory B, Westbrook, John D, Young, Jasmine, Yukich, Benjamin, Zardecki, Christine, Berman, Helen M, and Bourne, Philip E
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Bioengineering ,Generic health relevance ,Animals ,Computer Graphics ,Databases ,Protein ,Humans ,Internet ,Ligands ,Mice ,Protein Conformation ,Proteins ,Systems Integration ,User-Computer Interface ,Environmental Sciences ,Information and Computing Sciences ,Developmental Biology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.
- Published
- 2011
44. MRI in Practice
- Author
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Catherine Westbrook, John Talbot and Catherine Westbrook, John Talbot
- Published
- 2018
45. Digitizing Suzette: Creating a Framework for the Collaborative Analysis of an Historical French Textbook
- Author
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Westbrook, John, Jakacki, Diane, Heintzelman, Rebecca, Harnood, Juliya, Scholger, Walter, Vogeler, Georg, Tasovac, Toma, Baillot, Anne, Raunig, Elisabeth, Scholger, Martina, Steiner, Elisabeth, Centre for Information Modelling, and Helling, Patrick
- Subjects
Paper ,Textbooks ,History ,Long Presentation ,Cuisine ,Cultural studies ,Text Encoding and Analysis ,Education/ pedagogy ,semantic analysis ,Humanities computing ,text encoding and markup language creation ,deployment ,France ,and analysis ,Historical Data Analysis - Abstract
We present a collaborative framework using digital tools to analyze and present an important but neglected French belle-époque girls primary school reader, Marie Robert Halt's Suzette. Using our open data model, researchers can explore major themes (gender, class, etc.) and disciplinary topics (biology, cuisine, etc.) and propose new analytical frames
- Published
- 2023
- Full Text
- View/download PDF
46. Multiscale analyses on a massive immigration process of Sogatella furcifera (Horváth) in south-central China: influences of synoptic-scale meteorological conditions and topography
- Author
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Wu, Qiu-Lin, Westbrook, John K., Hu, Gao, Lu, Ming-Hong, Liu, Wan-Cai, Sword, Gregory A., and Zhai, Bao-Ping
- Published
- 2018
- Full Text
- View/download PDF
47. Exploring experimental structures and computed structure models from artificial intelligence/machine learning at RCSB Protein Data Bank (RCSB PDB, RCSB.org)
- Author
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Segura, Joan, primary, Duarte, Jose, additional, Bittrich, Sebastian, additional, Bi, Chunxiao, additional, Bhikadiya, Charmi, additional, Fayazi, Maryam, additional, Henry, Jeremy, additional, Khokhriakov, Igor, additional, Lowe, Robert, additional, Piehl, Dennis W., additional, Vallat, Brinda, additional, Voigt, Maria, additional, Westbrook, John, additional, Rose, Yana, additional, and Burley, Stephen K., additional
- Published
- 2023
- Full Text
- View/download PDF
48. Predator–prey interaction reveals local effects of high-altitude insect migration
- Author
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Krauel, Jennifer J., Brown, Veronica A., Westbrook, John K., and McCracken, Gary F.
- Published
- 2017
- Full Text
- View/download PDF
49. Airborne multispectral identification of individual cotton plants using consumer-grade cameras
- Author
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Westbrook, John K., Eyster, Ritchie S., Yang, Chenghai, and Suh, Charles P.-C.
- Published
- 2016
- Full Text
- View/download PDF
50. Gossypolhemiquinone, a dimeric sesquiterpenoid identified in cotton (Gossypium)
- Author
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Stipanovic, Robert, Puckhaber, Lorraine, Frelichowski, James, Jr., Esquivel, Jesus, Westbrook, John, O’Neil, Mike, Bell, Alois, Dowd, Michael, Hake, Kater, and Duke, Sara
- Published
- 2016
- Full Text
- View/download PDF
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