Search Results - "KLEYWEGT, Gerard J"

Highly accurate protein structure prediction for the human proteome by Tunyasuvunakool, Kathryn, Adler, Jonas, Wu, Zachary, Green, Tim, Zielinski, Michal, Žídek, Augustin, Bridgland, Alex, Cowie, Andrew, Meyer, Clemens, Laydon, Agata, Velankar, Sameer, Kleywegt, Gerard J., Bateman, Alex, Evans, Richard, Pritzel, Alexander, Figurnov, Michael, Ronneberger, Olaf, Bates, Russ, Kohl, Simon A. A., Potapenko, Anna, Ballard, Andrew J., Romera-Paredes, Bernardino, Nikolov, Stanislav, Jain, Rishub, Clancy, Ellen, Reiman, David, Petersen, Stig, Senior, Andrew W., Kavukcuoglu, Koray, Birney, Ewan, Kohli, Pushmeet, Jumper, John, Hassabis, Demis

“…Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based…”
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EMPIAR: a public archive for raw electron microscopy image data by Iudin, Andrii, Korir, Paul K, Salavert-Torres, José, Kleywegt, Gerard J, Patwardhan, Ardan

“…Raw 2D image data sets are often considerably larger than the final 3D reconstructions (gigabytes to terabytes versus megabytes to gigabytes), and their…”
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Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive by Burley, Stephen K, Berman, Helen M, Kleywegt, Gerard J, Markley, John L, Nakamura, Haruki, Velankar, Sameer

“…The Protein Data Bank (PDB)--the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes--was…”
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EMPIAR: the Electron Microscopy Public Image Archive by Iudin, Andrii, Korir, Paul K, Somasundharam, Sriram, Weyand, Simone, Cattavitello, Cesare, Fonseca, Neli, Salih, Osman, Kleywegt, Gerard J, Patwardhan, Ardan

“…Public archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and the Electron Microscopy…”
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Outcome of the First Electron Microscopy Validation Task Force Meeting by Henderson, Richard, Sali, Andrej, Baker, Matthew L., Carragher, Bridget, Devkota, Batsal, Downing, Kenneth H., Egelman, Edward H., Feng, Zukang, Frank, Joachim, Grigorieff, Nikolaus, Jiang, Wen, Ludtke, Steven J., Medalia, Ohad, Penczek, Pawel A., Rosenthal, Peter B., Rossmann, Michael G., Schmid, Michael F., Schröder, Gunnar F., Steven, Alasdair C., Stokes, David L., Westbrook, John D., Wriggers, Willy, Yang, Huanwang, Young, Jasmine, Berman, Helen M., Chiu, Wah, Kleywegt, Gerard J., Lawson, Catherine L.

“…This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the…”
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PDBe: improved findability of macromolecular structure data in the PDB by Armstrong, David R, Berrisford, John M, Conroy, Matthew J, Gutmanas, Aleksandras, Anyango, Stephen, Choudhary, Preeti, Clark, Alice R, Dana, Jose M, Deshpande, Mandar, Dunlop, Roisin, Gane, Paul, Gáborová, Romana, Gupta, Deepti, Haslam, Pauline, Koča, Jaroslav, Mak, Lora, Mir, Saqib, Mukhopadhyay, Abhik, Nadzirin, Nurul, Nair, Sreenath, Paysan-Lafosse, Typhaine, Pravda, Lukas, Sehnal, David, Salih, Osman, Smart, Oliver, Tolchard, James, Varadi, Mihaly, Svobodova-Vařeková, Radka, Zaki, Hossam, Kleywegt, Gerard J, Velankar, Sameer

“…Abstract The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition,…”
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Validation of Structures in the Protein Data Bank by Gore, Swanand, Sanz García, Eduardo, Hendrickx, Pieter M.S., Gutmanas, Aleksandras, Westbrook, John D., Yang, Huanwang, Feng, Zukang, Baskaran, Kumaran, Berrisford, John M., Hudson, Brian P., Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Mading, Steve, Mak, Lora, Mukhopadhyay, Abhik, Oldfield, Thomas J., Patwardhan, Ardan, Peisach, Ezra, Sahni, Gaurav, Sekharan, Monica R., Sen, Sanchayita, Shao, Chenghua, Smart, Oliver S., Ulrich, Eldon L., Yamashita, Reiko, Quesada, Martha, Young, Jasmine Y., Nakamura, Haruki, Markley, John L., Berman, Helen M., Burley, Stephen K., Velankar, Sameer, Kleywegt, Gerard J.

“…The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for…”
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A New Generation of Crystallographic Validation Tools for the Protein Data Bank by Read, Randy J., Adams, Paul D., Arendall, W. Bryan, Brunger, Axel T., Emsley, Paul, Joosten, Robbie P., Kleywegt, Gerard J., Krissinel, Eugene B., Lütteke, Thomas, Otwinowski, Zbyszek, Perrakis, Anastassis, Richardson, Jane S., Sheffler, William H., Smith, Janet L., Tickle, Ian J., Vriend, Gert, Zwart, Peter H.

“…This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current…”
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Recommendations of the wwPDB NMR Validation Task Force by Montelione, Gaetano T., Nilges, Michael, Bax, Ad, Güntert, Peter, Herrmann, Torsten, Richardson, Jane S., Schwieters, Charles D., Vranken, Wim F., Vuister, Geerten W., Wishart, David S., Berman, Helen M., Kleywegt, Gerard J., Markley, John L.

“…As methods for analysis of biomolecular structure and dynamics using nuclear magnetic resonance spectroscopy (NMR) continue to advance, the resulting 3D…”
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Implementing an X-ray validation pipeline for the Protein Data Bank by Gore, Swanand, Velankar, Sameer, Kleywegt, Gerard J.

“…There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed…”
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The Protein Data Bank archive as an open data resource by Berman, Helen M., Kleywegt, Gerard J., Nakamura, Haruki, Markley, John L.

“…The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012 ). An analysis of…”
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Whither structural biologists? by Kleywegt, Gerard J, Velankar, Sameer

“…The scientific impact of accurate protein-structure prediction methods is being felt already, but how might they affect the work and careers of structural…”
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PDBe: improved accessibility of macromolecular structure data from PDB and EMDB by Velankar, Sameer, van Ginkel, Glen, Alhroub, Younes, Battle, Gary M, Berrisford, John M, Conroy, Matthew J, Dana, Jose M, Gore, Swanand P, Gutmanas, Aleksandras, Haslam, Pauline, Hendrickx, Pieter M S, Lagerstedt, Ingvar, Mir, Saqib, Fernandez Montecelo, Manuel A, Mukhopadhyay, Abhik, Oldfield, Thomas J, Patwardhan, Ardan, Sanz-García, Eduardo, Sen, Sanchayita, Slowley, Robert A, Wainwright, Michael E, Deshpande, Mandar S, Iudin, Andrii, Sahni, Gaurav, Salavert Torres, Jose, Hirshberg, Miriam, Mak, Lora, Nadzirin, Nurul, Armstrong, David R, Clark, Alice R, Smart, Oliver S, Korir, Paul K, Kleywegt, Gerard J

“…The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches,…”
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An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD by Yusuf, Dilmurat, Davis, Andrew M, Kleywegt, Gerard J, Schmitt, Stefan

“…A new assessment criterion for docking poses is proposed in which experimental electron density is taken into account when evaluating the ability of docking…”
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Resolution of ab initio shapes determined from small-angle scattering by Tuukkanen, Anne T, Kleywegt, Gerard J, Svergun, Dmitri I

“…Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron…”
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The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future by Berman, Helen M., Kleywegt, Gerard J., Nakamura, Haruki, Markley, John L.

“…A symposium celebrating the 40th anniversary of the Protein Data Bank archive (PDB), organized by the Worldwide Protein Data Bank, was held at Cold Spring…”
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Validation of ligands in macromolecular structures determined by X‐ray crystallography by Smart, Oliver S., Horský, Vladimír, Gore, Swanand, Svobodová Vařeková, Radka, Bendová, Veronika, Kleywegt, Gerard J., Velankar, Sameer

“…Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure‐guided drug discovery and…”
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Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB by Trewhella, Jill, Hendrickson, Wayne A., Kleywegt, Gerard J., Sali, Andrej, Sato, Mamoru, Schwede, Torsten, Svergun, Dmitri I., Tainer, John A., Westbrook, John, Berman, Helen M.

“…This report presents the conclusions of the July 12–13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman…”
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PSICQUIC and PSISCORE: accessing and scoring molecular interactions by Aranda, Bruno, Blankenburg, Hagen, Kerrien, Samuel, Brinkman, Fiona S L, Ceol, Arnaud, Chautard, Emilie, Dana, Jose M, De Las Rivas, Javier, Dumousseau, Marine, Galeota, Eugenia, Gaulton, Anna, Goll, Johannes, Hancock, Robert E W, Isserlin, Ruth, Jimenez, Rafael C, Kerssemakers, Jules, Khadake, Jyoti, Lynn, David J, Michaut, Magali, O'Kelly, Gavin, Ono, Keiichiro, Orchard, Sandra, Prieto, Carlos, Razick, Sabry, Rigina, Olga, Salwinski, Lukasz, Simonovic, Milan, Velankar, Sameer, Winter, Andrew, Wu, Guanming, Bader, Gary D, Cesareni, Gianni, Donaldson, Ian M, Eisenberg, David, Kleywegt, Gerard J, Overington, John, Ricard-Blum, Sylvie, Tyers, Mike, Albrecht, Mario, Hermjakob, Henning

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PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education by Varadi, Mihaly, Anyango, Stephen, Appasamy, Sri Devan, Armstrong, David, Bage, Marcus, Berrisford, John, Choudhary, Preeti, Bertoni, Damian, Deshpande, Mandar, Leines, Grisell Diaz, Ellaway, Joseph, Evans, Genevieve, Gaborova, Romana, Gupta, Deepti, Gutmanas, Aleksandras, Harrus, Deborah, Kleywegt, Gerard J., Bueno, Weslley Morellato, Nadzirin, Nurul, Nair, Sreenath, Pravda, Lukas, Afonso, Marcelo Querino Lima, Sehnal, David, Tanweer, Ahsan, Tolchard, James, Abrams, Charlotte, Dunlop, Roisin, Velankar, Sameer

“…The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task…”
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