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1. Community recommendations on cryoEM data archiving and validation

Author

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

Subjects
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.

Published
2024

2. Community recommendations on cryoEM data archiving and validation

Author

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

Subjects
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

Published
2023
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3. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Author

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

Subjects
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).

Published
2019

4. Community recommendations on cryoEM data archiving and validation

Author

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

5. Community recommendations on cryoEM data archiving and validation

Author

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
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6. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Author

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

7. Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies.

Author

Ellaway, Joseph I. J., Anyango, Stephen, Nair, Sreenath, Zaki, Hossam A., Nadzirin, Nurul, Powell, Harold R., Gutmanas, Aleksandras, Varadi, Mihaly, and Velankar, Sameer

Subjects
BANKING industry, DRUG discovery, PROTEIN conformation, CONFORMATIONAL analysis, ARTIFICIAL intelligence, PROTEIN structure
Abstract

Studying protein dynamics and conformational heterogeneity is crucial for understanding biomolecular systems and treating disease. Despite the deposition of over 215 000 macromolecular structures in the Protein Data Bank and the advent of AI-based structure prediction tools such as AlphaFold2, RoseTTAFold, and ESMFold, static representations are typically produced, which fail to fully capture macromolecular motion. Here, we discuss the importance of integrating experimental structures with computational clustering to explore the conformational landscapes that manifest protein function. We describe the method developed by the Protein Data Bank in Europe – Knowledge Base to identify distinct conformational states, demonstrate the resource's primary use cases, through examples, and discuss the need for further efforts to annotate protein conformations with functional information. Such initiatives will be crucial in unlocking the potential of protein dynamics data, expediting drug discovery research, and deepening our understanding of macromolecular mechanisms. [ABSTRACT FROM AUTHOR]

Published
2024
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9. PDBe and PDBe‐KB : Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education

Author

Varadi, Mihaly, primary, Anyango, Stephen, additional, Appasamy, Sri Devan, additional, Armstrong, David, additional, Bage, Marcus, additional, Berrisford, John, additional, Choudhary, Preeti, additional, Bertoni, Damian, additional, Deshpande, Mandar, additional, Leines, Grisell Diaz, additional, Ellaway, Joseph, additional, Evans, Genevieve, additional, Gaborova, Romana, additional, Gupta, Deepti, additional, Gutmanas, Aleksandras, additional, Harrus, Deborah, additional, Kleywegt, Gerard J., additional, Bueno, Weslley Morellato, additional, Nadzirin, Nurul, additional, Nair, Sreenath, additional, Pravda, Lukas, additional, Afonso, Marcelo Querino Lima, additional, Sehnal, David, additional, Tanweer, Ahsan, additional, Tolchard, James, additional, Abrams, Charlotte, additional, Dunlop, Roisin, additional, and Velankar, Sameer, additional

Published
2022
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15. PDBe: Protein Data Bank in Europe

Author

Gutmanas, Aleksandras, Alhroub, Younes, Battle, Gary M., Berrisford, John M., Bochet, Estelle, Conroy, Matthew J., Dana, Jose M., Fernandez Montecelo, Manuel A., van Ginkel, Glen, Gore, Swanand P., Haslam, Pauline, Hatherley, Rowan, Hendrickx, Pieter M.S., Hirshberg, Miriam, Lagerstedt, Ingvar, Mir, Saqib, Mukhopadhyay, Abhik, Oldfield, Thomas J., Patwardhan, Ardan, Rinaldi, Luana, Sahni, Gaurav, Sanz-García, Eduardo, Sen, Sanchayita, Slowley, Robert A., Velankar, Sameer, Wainwright, Michael E., and Kleywegt, Gerard J.

Published
2014
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16. An intrinsically disordered proteins community for ELIXIR

Author

Davey, Norman E., Felli, Isabella C., Gibson, Toby J., Gutmanas, Aleksandras, Hancock, John M., Harrow, Jen, Higgins, Desmond, Jeffries, Cy M., Le Mercier, Philippe, Mészáros, Balint, Necci, Marco, Babu, M. Madan, Notredame, Cedric, Orchard, Sandra, Ouzounis, Christos A., Pancsa, Rita, Papaleo, Elena, Pierattelli, Roberta, Piovesan, Damiano, Promponas, Vasilis J., Ruch, Patrick, Rustici, Gabriella, Blackledge, Martin, Romero, Pedro, Sarntivijai, Sirarat, Saunders, Gary, Schuler, Benjamin, Sharan, Malvika, Shields, Denis C., Sussman, Joel L., Tedds, Jonathan A., Tompa, Peter, Turewicz, Michael, Bridge, Alan, Vondrasek, Jiri, Vranken, Wim F., Wallace, Bonnie Ann, Wichapong, Kanin, Tosatto, Silvio C. E., Capella-Gutierrez, Salvador, Dosztanyi, Zsuzsanna, Drysdale, Rachel, Edwards, Richard J., Elofsson, Arne, Capella-Gutierrez, Salvador [0000-0002-0309-604X], Elofsson, Arne [0000-0002-7115-9751], Gutmanas, Aleksandras [0000-0001-6311-0176], Hancock, John M [0000-0003-2991-2217], Le Mercier, Philippe [0000-0001-8528-090X], Orchard, Sandra [0000-0002-8878-3972], Pierattelli, Roberta [0000-0001-7755-0885], Promponas, Vasilis J [0000-0003-3352-4831], Romero, Pedro [0000-0002-6995-5193], Turewicz, Michael [0000-0003-0737-1114], Apollo - University of Cambridge Repository, Biochemie, RS: Carim - B01 Blood proteins & engineering, RS: CARIM - R1 - Thrombosis and haemostasis, Promponas, Vasilis J. [0000-0003-3352-4831], Faculty of Sciences and Bioengineering Sciences, Department of Bio-engineering Sciences, Structural Biology Brussels, Basic (bio-) Medical Sciences, Chemistry, and Informatics and Applied Informatics

Subjects
0301 basic medicine, databases, community standards, protein-protein interactions, bcs, Intrinsically disordered proteins, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, White paper, Blueprint, General Pharmacology, Toxicology and Pharmaceutics, Community standards, computer.programming_language, 030102 biochemistry & molecular biology, General Immunology and Microbiology, cellular regulation, Cellular Regulation, Intrinsically Disordered Proteins/metabolism, General Medicine, Benchmarking, Articles, Opinion Article, protein function, Elixir, Data science, ELIXIR, Intrinsically Disordered Proteins, Identification (information), 030104 developmental biology, protein dynamics, Elixir (programming language), computer, Data Annotation
Abstract

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders. BW was funded by a grant from the BBSRC [BB/P024092/1]. AB, SO and PLM were supported by the National Eye Institute (NEI), National Human Genome Research Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of General Medical Sciences (NIGMS), and National Institute of Mental Health (NIMH) of the National Institutes of Health under Award Number [U24HG007822] (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health), by European Molecular Biology Laboratory (EMBL) and by the Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI. AG was supported by the European Molecular Biology Laboratory (EMBL) and the Wellcome Trust [104948]. AE was supported by a Vetenskapsrådet grant [2016-03798]. EP was supported by Danmarks Grundforskningsfond [DNRF125] and a Carlsberg Foundation Distinguished Fellowship [CF18-0314]. JLS was supported by the Israel I-CORE Project: Integrated Structural Cell Biology and by Instruct-ERIC. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement [778247] and COST Action BM1405 NGP-net.

Published
2019

18. PDBe: Protein Data Bank in Europe

Author

Velankar, Sameer, Alhroub, Younes, Alili, Anaëlle, Best, Christoph, Boutselakis, Harry C., Caboche, Ségolène, Conroy, Matthew J., Dana, Jose M., van Ginkel, Glen, Golovin, Adel, Gore, Swanand P., Gutmanas, Aleksandras, Haslam, Pauline, Hirshberg, Miriam, John, Melford, Lagerstedt, Ingvar, Mir, Saqib, Newman, Laurence E., Oldfield, Tom J., Penkett, Chris J., Pineda-Castillo, Jorge, Rinaldi, Luana, Sahni, Gaurav, Sawka, Grégoire, Sen, Sanchayita, Slowley, Robert, Sousa da Silva, Alan Wilter, Suarez-Uruena, Antonio, Swaminathan, G. Jawahar, Symmons, Martyn F., Vranken, Wim F., Wainwright, Michael, and Kleywegt, Gerard J.

Published
2011
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20. An intrinsically disordered proteins community for ELIXIR

Author

Davey, Norman E, Babu, M Madan, Blackledge, Martin, Bridge, Alan, Capella-Gutierrez, Salvador, Dosztanyi, Zsuzsanna, Drysdale, Rachel, Edwards, Richard J, Elofsson, Arne, Felli, Isabella C, Gibson, Toby J, Gutmanas, Aleksandras, Hancock, John M, Harrow, Jen, Higgins, Desmond, Jeffries, Cy M, Le Mercier, Philippe, Mészáros, Balint, Necci, Marco, Notredame, Cedric, Orchard, Sandra, Ouzounis, Christos A, Pancsa, Rita, Papaleo, Elena, Pierattelli, Roberta, Piovesan, Damiano, Promponas, Vasilis J, Ruch, Patrick, Rustici, Gabriella, Romero, Pedro, et al, University of Zurich, and Davey, Norman E

Subjects
1300 General Biochemistry, Genetics and Molecular Biology, 2400 General Immunology and Microbiology, 10019 Department of Biochemistry, 570 Life sciences, biology, 610 Medicine & health, 3000 General Pharmacology, Toxicology and Pharmaceutics
Published
2019

22. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Author

Afonine, Pavel, Afonine, Pavel, Baskaran, Kumaran, Berman, Helen, Berrisford, John, Bricogne, Gerard, Brown, David, Burley, Stephen, Chen, Minyu, Feng, Zukang, Flensburg, Claus, Gutmanas, Aleksandras, Hoch, Jeffrey, Ikegawa, Yasuyo, Kengaku, Yumiko, Krissinel, Eugene, Kurisu, Genji, Liang, Yuhe, Ulrich, Eldon, Velankar, Sameer, Vonrhein, Clemens, Westbrook, John, Wojdyr, Marcin, Yokochi, Masashi, Young, Jasmine, Murshudov, Garib, Noble, Martin, Peisach, Ezra, Persikova, Irina, Mak, Lora, Markley, John, Moriarty, Nigel, Poon, Billy, Sobolev, Oleg, Liebschner, Dorothee, Adams, Paul, Afonine, Pavel, Afonine, Pavel, Baskaran, Kumaran, Berman, Helen, Berrisford, John, Bricogne, Gerard, Brown, David, Burley, Stephen, Chen, Minyu, Feng, Zukang, Flensburg, Claus, Gutmanas, Aleksandras, Hoch, Jeffrey, Ikegawa, Yasuyo, Kengaku, Yumiko, Krissinel, Eugene, Kurisu, Genji, Liang, Yuhe, Ulrich, Eldon, Velankar, Sameer, Vonrhein, Clemens, Westbrook, John, Wojdyr, Marcin, Yokochi, Masashi, Young, Jasmine, Murshudov, Garib, Noble, Martin, Peisach, Ezra, Persikova, Irina, Mak, Lora, Markley, John, Moriarty, Nigel, Poon, Billy, Sobolev, Oleg, Liebschner, Dorothee, and Adams, Paul

Abstract

This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).

Published
2019

23. PDBe: improved findability of macromolecular structure data in the PDB

Author

Armstrong, David R, primary, Berrisford, John M, additional, Conroy, Matthew J, additional, Gutmanas, Aleksandras, additional, Anyango, Stephen, additional, Choudhary, Preeti, additional, Clark, Alice R, additional, Dana, Jose M, additional, Deshpande, Mandar, additional, Dunlop, Roisin, additional, Gane, Paul, additional, Gáborová, Romana, additional, Gupta, Deepti, additional, Haslam, Pauline, additional, Koča, Jaroslav, additional, Mak, Lora, additional, Mir, Saqib, additional, Mukhopadhyay, Abhik, additional, Nadzirin, Nurul, additional, Nair, Sreenath, additional, Paysan-Lafosse, Typhaine, additional, Pravda, Lukas, additional, Sehnal, David, additional, Salih, Osman, additional, Smart, Oliver, additional, Tolchard, James, additional, Varadi, Mihaly, additional, Svobodova-Vařeková, Radka, additional, Zaki, Hossam, additional, Kleywegt, Gerard J, additional, and Velankar, Sameer, additional

Published
2019
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24. PDBe: improved findability of macromolecular structure data in the PDB.

Author

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, and Nair, Sreenath

Published
2020
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26. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Author

Young, Jasmine Y, primary, Westbrook, John D, additional, Feng, Zukang, additional, Peisach, Ezra, additional, Persikova, Irina, additional, Sala, Raul, additional, Sen, Sanchayita, additional, Berrisford, John M, additional, Swaminathan, G Jawahar, additional, Oldfield, Thomas J, additional, Gutmanas, Aleksandras, additional, Igarashi, Reiko, additional, Armstrong, David R, additional, Baskaran, Kumaran, additional, Chen, Li, additional, Chen, Minyu, additional, Clark, Alice R, additional, Di Costanzo, Luigi, additional, Dimitropoulos, Dimitris, additional, Gao, Guanghua, additional, Ghosh, Sutapa, additional, Gore, Swanand, additional, Guranovic, Vladimir, additional, Hendrickx, Pieter M S, additional, Hudson, Brian P, additional, Ikegawa, Yasuyo, additional, Kengaku, Yumiko, additional, Lawson, Catherine L, additional, Liang, Yuhe, additional, Mak, Lora, additional, Mukhopadhyay, Abhik, additional, Narayanan, Buvaneswari, additional, Nishiyama, Kayoko, additional, Patwardhan, Ardan, additional, Sahni, Gaurav, additional, Sanz-García, Eduardo, additional, Sato, Junko, additional, Sekharan, Monica R, additional, Shao, Chenghua, additional, Smart, Oliver S, additional, Tan, Lihua, additional, van Ginkel, Glen, additional, Yang, Huanwang, additional, Zhuravleva, Marina A, additional, Markley, John L, additional, Nakamura, Haruki, additional, Kurisu, Genji, additional, Kleywegt, Gerard J, additional, Velankar, Sameer, additional, Berman, Helen M, additional, and Burley, Stephen K, additional

Published
2018
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27. Validation of Structures in the Protein Data Bank

Author

Gore, Swanand, primary, Sanz García, Eduardo, additional, Hendrickx, Pieter M.S., additional, Gutmanas, Aleksandras, additional, Westbrook, John D., additional, Yang, Huanwang, additional, Feng, Zukang, additional, Baskaran, Kumaran, additional, Berrisford, John M., additional, Hudson, Brian P., additional, Ikegawa, Yasuyo, additional, Kobayashi, Naohiro, additional, Lawson, Catherine L., additional, Mading, Steve, additional, Mak, Lora, additional, Mukhopadhyay, Abhik, additional, Oldfield, Thomas J., additional, Patwardhan, Ardan, additional, Peisach, Ezra, additional, Sahni, Gaurav, additional, Sekharan, Monica R., additional, Sen, Sanchayita, additional, Shao, Chenghua, additional, Smart, Oliver S., additional, Ulrich, Eldon L., additional, Yamashita, Reiko, additional, Quesada, Martha, additional, Young, Jasmine Y., additional, Nakamura, Haruki, additional, Markley, John L., additional, Berman, Helen M., additional, Burley, Stephen K., additional, Velankar, Sameer, additional, and Kleywegt, Gerard J., additional

Published
2017
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29. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Author

Mir, Saqib, primary, Alhroub, Younes, additional, Anyango, Stephen, additional, Armstrong, David R, additional, Berrisford, John M, additional, Clark, Alice R, additional, Conroy, Matthew J, additional, Dana, Jose M, additional, Deshpande, Mandar, additional, Gupta, Deepti, additional, Gutmanas, Aleksandras, additional, Haslam, Pauline, additional, Mak, Lora, additional, Mukhopadhyay, Abhik, additional, Nadzirin, Nurul, additional, Paysan-Lafosse, Typhaine, additional, Sehnal, David, additional, Sen, Sanchayita, additional, Smart, Oliver S, additional, Varadi, Mihaly, additional, Kleywegt, Gerard J, additional, and Velankar, Sameer, additional

Published
2017
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30. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Author

Young, Jasmine Y., primary, Westbrook, John D., additional, Feng, Zukang, additional, Sala, Raul, additional, Peisach, Ezra, additional, Oldfield, Thomas J., additional, Sen, Sanchayita, additional, Gutmanas, Aleksandras, additional, Armstrong, David R., additional, Berrisford, John M., additional, Chen, Li, additional, Chen, Minyu, additional, Di Costanzo, Luigi, additional, Dimitropoulos, Dimitris, additional, Gao, Guanghua, additional, Ghosh, Sutapa, additional, Gore, Swanand, additional, Guranovic, Vladimir, additional, Hendrickx, Pieter M.S., additional, Hudson, Brian P., additional, Igarashi, Reiko, additional, Ikegawa, Yasuyo, additional, Kobayashi, Naohiro, additional, Lawson, Catherine L., additional, Liang, Yuhe, additional, Mading, Steve, additional, Mak, Lora, additional, Mir, M. Saqib, additional, Mukhopadhyay, Abhik, additional, Patwardhan, Ardan, additional, Persikova, Irina, additional, Rinaldi, Luana, additional, Sanz-Garcia, Eduardo, additional, Sekharan, Monica R., additional, Shao, Chenghua, additional, Swaminathan, G. Jawahar, additional, Tan, Lihua, additional, Ulrich, Eldon L., additional, van Ginkel, Glen, additional, Yamashita, Reiko, additional, Yang, Huanwang, additional, Zhuravleva, Marina A., additional, Quesada, Martha, additional, Kleywegt, Gerard J., additional, Berman, Helen M., additional, Markley, John L., additional, Nakamura, Haruki, additional, Velankar, Sameer, additional, and Burley, Stephen K., additional

Published
2017
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32. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Author

Sub NMR Spectroscopy, NMR Spectroscopy, Sali, Andrej, Berman, Helen M., Schwede, Torsten, Trewhella, Jill, Kleywegt, Gerard, Burley, Stephen K., Markley, John, Nakamura, Haruki, Adams, Paul, Bonvin, Alexandre M J J, 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 A M, Svergun, Dmitri, Topf, Maya, Ulrich, Eldon L., Velankar, Sameer, Westbrook, John D., Sub NMR Spectroscopy, NMR Spectroscopy, Sali, Andrej, Berman, Helen M., Schwede, Torsten, Trewhella, Jill, Kleywegt, Gerard, Burley, Stephen K., Markley, John, Nakamura, Haruki, Adams, Paul, Bonvin, Alexandre M J J, 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 A M, Svergun, Dmitri, Topf, Maya, Ulrich, Eldon L., Velankar, Sameer, and Westbrook, John D.

Published
2015

33. NMR Exchange Format: A unified and open standard for representation of NMR restraint data

Author

Gutmanas, Aleksandras, Kleywegt, Gerard Jacob, Kobayashi, Naohiro, Lange, Oliver O.F., Markley, John J.L., Montelione, Gaetano Thomas, Nilges, Michael, Ragan, Timothy T.J., Schwieters, Charles C.D., Tejero, Roberto, Ulrich, Eldon E.L., Adams, Paul P.D., Velankar, Sameer, Vranken, Wim, Wedell, Jonathan J.R., Westbrook, John, Wishart, David D.S., Vuister, Geerten W, Bardiaux, Benjamin, Berman, Helen, Case, David D.A., Fogh, Rasmus R.H., Güntert, Peter, Hendrickx, Pieter M S, Herrmann, Torsten, Gutmanas, Aleksandras, Kleywegt, Gerard Jacob, Kobayashi, Naohiro, Lange, Oliver O.F., Markley, John J.L., Montelione, Gaetano Thomas, Nilges, Michael, Ragan, Timothy T.J., Schwieters, Charles C.D., Tejero, Roberto, Ulrich, Eldon E.L., Adams, Paul P.D., Velankar, Sameer, Vranken, Wim, Wedell, Jonathan J.R., Westbrook, John, Wishart, David D.S., Vuister, Geerten W, Bardiaux, Benjamin, Berman, Helen, Case, David D.A., Fogh, Rasmus R.H., Güntert, Peter, Hendrickx, Pieter M S, and Herrmann, Torsten

Abstract

SCOPUS: le.j, info:eu-repo/semantics/published

Published
2015

34. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Author

Velankar, Sameer, primary, van Ginkel, Glen, additional, Alhroub, Younes, additional, Battle, Gary M., additional, Berrisford, John M., additional, Conroy, Matthew J., additional, Dana, Jose M., additional, Gore, Swanand P., additional, Gutmanas, Aleksandras, additional, Haslam, Pauline, additional, Hendrickx, Pieter M. S., additional, Lagerstedt, Ingvar, additional, Mir, Saqib, additional, Fernandez Montecelo, Manuel A., additional, Mukhopadhyay, Abhik, additional, Oldfield, Thomas J., additional, Patwardhan, Ardan, additional, Sanz-García, Eduardo, additional, Sen, Sanchayita, additional, Slowley, Robert A., additional, Wainwright, Michael E., additional, Deshpande, Mandar S., additional, Iudin, Andrii, additional, Sahni, Gaurav, additional, Salavert Torres, Jose, additional, Hirshberg, Miriam, additional, Mak, Lora, additional, Nadzirin, Nurul, additional, Armstrong, David R., additional, Clark, Alice R., additional, Smart, Oliver S., additional, Korir, Paul K., additional, and Kleywegt, Gerard J., additional

Published
2015
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35. Straightforward and complete deposition of NMR data to the PDBe

Author

Penkett, Christopher, Van Ginkel, Glen, Velankar, Sameer, Swaminathan, G, Ulrich, Eldon, Mading, Steve, Stevens, Tim, Fogh, Rasmus, Gutmanas, Aleksandras, Kleywegt, Gerard, Henrick, Kim, Vranken, Wim, and Department of Bio-engineering Sciences

Subjects
NMR structure validation, CCPN, Database deposition
Abstract

We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/ pdbe/nmr/deposition/eci.html.

Published
2010

36. NMR Exchange Format: a unified and open standard for representation of NMR restraint data

Author

Gutmanas, Aleksandras, primary, Adams, Paul D, additional, Bardiaux, Benjamin, additional, Berman, Helen M, additional, Case, David A, additional, Fogh, Rasmus H, additional, Güntert, Peter, additional, Hendrickx, Pieter M S, additional, Herrmann, Torsten, additional, Kleywegt, Gerard J, additional, Kobayashi, Naohiro, additional, Lange, Oliver F, additional, Markley, John L, additional, Montelione, Gaetano T, additional, Nilges, Michael, additional, Ragan, Timothy J, additional, Schwieters, Charles D, additional, Tejero, Roberto, additional, Ulrich, Eldon L, additional, Velankar, Sameer, additional, Vranken, Wim F, additional, Wedell, Jonathan R, additional, Westbrook, John, additional, Wishart, David S, additional, and Vuister, Geerten W, additional

Published
2015
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37. Structural Characterization of a Flexible Two-Domain Protein in Solution Using Small Angle X-Ray Scattering and NMR Data

Author

Lemak, Alexander, primary, Wu, Bin, additional, Yee, Adelinda, additional, Houliston, Scott, additional, Lee, Hsiau-Wei, additional, Gutmanas, Aleksandras, additional, Fang, Xianyang, additional, Garcia, Maite, additional, Semesi, Anthony, additional, Wang, Yun-Xing, additional, Prestegard, James H., additional, and Arrowsmith, Cheryl H., additional

Published
2014
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38. PDBe: Protein Data Bank in Europe

Author

Gutmanas, Aleksandras, primary, Alhroub, Younes, additional, Battle, Gary M., additional, Berrisford, John M., additional, Bochet, Estelle, additional, Conroy, Matthew J., additional, Dana, Jose M., additional, Fernandez Montecelo, Manuel A., additional, van Ginkel, Glen, additional, Gore, Swanand P., additional, Haslam, Pauline, additional, Hatherley, Rowan, additional, Hendrickx, Pieter M.S., additional, Hirshberg, Miriam, additional, Lagerstedt, Ingvar, additional, Mir, Saqib, additional, Mukhopadhyay, Abhik, additional, Oldfield, Thomas J., additional, Patwardhan, Ardan, additional, Rinaldi, Luana, additional, Sahni, Gaurav, additional, Sanz-García, Eduardo, additional, Sen, Sanchayita, additional, Slowley, Robert A., additional, Velankar, Sameer, additional, Wainwright, Michael E., additional, and Kleywegt, Gerard J., additional

Published
2013
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42. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Author

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, and Slowley, Robert A.

Published
2016
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43. Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Author

Rosato, Antonio, primary, Aramini, James M., additional, Arrowsmith, Cheryl, additional, Bagaria, Anurag, additional, Baker, David, additional, Cavalli, Andrea, additional, Doreleijers, Jurgen F., additional, Eletsky, Alexander, additional, Giachetti, Andrea, additional, Guerry, Paul, additional, Gutmanas, Aleksandras, additional, Güntert, Peter, additional, He, Yunfen, additional, Herrmann, Torsten, additional, Huang, Yuanpeng J., additional, Jaravine, Victor, additional, Jonker, Hendrik R.A., additional, Kennedy, Michael A., additional, Lange, Oliver F., additional, Liu, Gaohua, additional, Malliavin, Thérèse E., additional, Mani, Rajeswari, additional, Mao, Binchen, additional, Montelione, Gaetano T., additional, Nilges, Michael, additional, Rossi, Paolo, additional, van der Schot, Gijs, additional, Schwalbe, Harald, additional, Szyperski, Thomas A., additional, Vendruscolo, Michele, additional, Vernon, Robert, additional, Vranken, Wim F., additional, de Vries, Sjoerd, additional, Vuister, Geerten W., additional, Wu, Bin, additional, Yang, Yunhuang, additional, and Bonvin, Alexandre M.J.J., additional

Published
2012
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46. Solution NMR in structural genomics

Author

Yee, Adelinda, Gutmanas, Aleksandras, and Arrowsmith, Cheryl H

Subjects
*PROTEOMICS, *GLOBULAR proteins, *AMINO acid sequence, *PROTEIN folding, *NUCLEAR magnetic resonance spectroscopy, *GENOMICS
Abstract

Structural genomics (also known as structural proteomics) aims to generate accurate three-dimensional models for all folded, globular proteins and domains in the protein universe to understand the relationship between protein sequence, structure and function. NMR spectroscopy of small (<20kDa) proteins has been used successfully within several large-scale structural genomics projects for more than six years now. Recent advances coming from traditional NMR structural biology laboratories as well as large scale centers and consortia using NMR for structural genomics promise to facilitate NMR analysis making it even a more efficient and increasingly automated procedure. [Copyright &y& Elsevier]

Published
2006
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47. Three-way decomposition of a complete 3D 15N-NOESY-HSQC.

Author

Gutmanas, Aleksandras, Jarvoll, Patrik, Orekhov, Vladislav Yu., and Billeter, Martin

Subjects
PROTEINS, AMIDES, ALGORITHMS, BIOMOLECULES, ORGANIC compounds, PHYSICAL sciences
Abstract

Three-way decomposition is applied for the structural analysis of a complete three-dimensional 15N-NOESY-HSQC of the 128 residues long protein azurin. The procedure presented includes decomposition using the software MUNIN, providing an initial characterization of the complete spectrum by 355 components. This is followed by post-processing yielding a final list of 149 components, 123 of which characterize 1859 NOE peaks from backbone N-H groups. Components from three-way decomposition are defined as direct products of one-dimensional shapes along the three dimensions. Thus, a complete set of distance constraints from this spectrum is obtained by one-dimensional peak picking of the shapes along the NOE dimension. Correctness and completeness of this set of NOEs are tested for all backbone amide groups against both an independent peak picking algorithm and the three-dimensional crystal structure of azurin, and a coincidence of about 95% is observed. Automated `demixing' of components that are `mixed' in a complex manner due to overlap of the HN and/or 15N frequencies is illustrated. [ABSTRACT FROM AUTHOR]

Published
2002
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48. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation.

Author

Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, and Velankar S

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 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 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.

Published
2024

49. An intrinsically disordered proteins community for ELIXIR.

Author

Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, and Tosatto SCE

Subjects
Intrinsically Disordered Proteins metabolism
Abstract

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders., Competing Interests: No competing interests were disclosed., (Copyright: © 2019 Davey NE et al.)

Published
2019
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50. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Author

Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, and Velankar S

Subjects
Amino Acid Sequence, Computer Graphics, Databases as Topic, Europe, Humans, Information Dissemination, Internet, Models, Molecular, Molecular Sequence Annotation, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Proteins genetics, Proteins metabolism, Computational Biology methods, Databases, Protein, Proteins chemistry, Sequence Analysis, Protein methods, User-Computer Interface
Abstract

The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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