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2. The Inverse Gamma Distribution and Benford's Law

Author

Durst, Rebecca F., Huynh, Chi, Lott, Adam, Miller, Steven J., Palsson, Eyvindur A., Touw, Wouter, and Vriend, Gert

Subjects
Mathematics - Probability, 60F05, 11K06 (primary), 60E10, 42A16, 62E15, 62P99 (secondary)
Abstract

According to Benford's Law, many data sets have a bias towards lower leading digits (about $30\%$ are $1$'s). The applications of Benford's Law vary: from detecting tax, voter and image fraud to determining the possibility of match-fixing in competitive sports. There are many common distributions that exhibit such bias, i.e. they are almost Benford. These include the exponential and the Weibull distributions. Motivated by these examples and the fact that the underlying distribution of factors in protein structure follows an inverse gamma distribution, we determine the closeness of this distribution to a Benford distribution as its parameters change., Comment: Version 1.1.2, 14 pages, 10 figures

Published
2016

6. Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator

Author

Lounnas, Valère, Wedler, Henry B., Newman, Timothy, Black, Jon, Vriend, Gert, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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8. The bio.tools registry of software tools and data resources for the life sciences

Author

Ison, Jon, Ienasescu, Hans, Chmura, Piotr, Rydza, Emil, Ménager, Hervé, Kalaš, Matúš, Schwämmle, Veit, Grüning, Björn, Beard, Niall, Lopez, Rodrigo, Duvaud, Severine, Stockinger, Heinz, Persson, Bengt, Vařeková, Radka Svobodová, Raček, Tomáš, Vondrášek, Jiří, Peterson, Hedi, Salumets, Ahto, Jonassen, Inge, Hooft, Rob, Nyrönen, Tommi, Valencia, Alfonso, Capella, Salvador, Gelpí, Josep, Zambelli, Federico, Savakis, Babis, Leskošek, Brane, Rapacki, Kristoffer, Blanchet, Christophe, Jimenez, Rafael, Oliveira, Arlindo, Vriend, Gert, Collin, Olivier, van Helden, Jacques, Løngreen, Peter, and Brunak, Søren

Published
2019
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12. Structural anomalies in a published NMR-derived structure of IRAK-M

Author

Poelman, Hessel, Ippel, Hans, Gürkan, Berke, Boelens, Rolf, Vriend, Gert, Veer, Cornelis van ‘t, Lutgens, Esther, Nicolaes, Gerry A.F., Sub Algemeen Scheikunde, Afd Scheikunde Algemeen, Sub Algemeen Scheikunde, Afd Scheikunde Algemeen, Biochemie, RS: Carim - B01 Blood proteins & engineering, Graduate School, ACS - Atherosclerosis & ischemic syndromes, Center of Experimental and Molecular Medicine, and ACS - Pulmonary hypertension & thrombosis

Subjects
Structure (category theory), 5UKE, Crystal structure, Protein Structure, Secondary, 03 medical and health sciences, 0302 clinical medicine, Taverne, Side chain, IRAK-M, Materials Chemistry, Homology modeling, Physical and Theoretical Chemistry, Spectroscopy, 030304 developmental biology, Death domain, Physics, WHAT_CHECK, 0303 health sciences, TALOS-N, Structure validation, Yasara, Computer Graphics and Computer-Aided Design, NMR, Crystallography, DALI, Myddosome, Docking (molecular), 030220 oncology & carcinogenesis, Torsion (algebra), Signal Transduction
Abstract

Signaling by Toll-Like Receptors and the Interleukin-1 Receptor (IL1-R) involves intracellular binding of MyD88, followed by assembly of IL1-R Associated Kinases (IRAKs) into the so-called Myddosome. Using NMR, Nechama et al. determined the structure of the IRAK-M death domain monomer (PDBid: 5UKE). With this structure, they performed a docking study to model the location of IRAK-M in the Myddosome. Based on this, they present a molecular basis for selectivity of IRAK-M towards IRAK1 over IRAK2 binding. When we attempted to use 5UKE as a homology modeling template, we noticed that our 5UKE-based models had structural issues, such as disallowed torsion angles and solvent exposed tryptophans. We therefore analyzed the NMR ensemble of 5UKE using structure validation tools and we compared 5UKE with homologous high-resolution X-ray structures. We identified several structural anomalies in 5UKE, including packing issues, frayed helices and improbable side chain conformations. We used Yasara to build a homology model, based on two high resolution death domain crystal structures, as an alternative model for the IRAK-M death domain (atomic coordinates, modeling details and validation are available at https://swift.cmbi.umcn.nl/gv/service/5uke/). Our model agrees better with known death domain structure information than 5UKE and also with the chemical shift data that was deposited for 5UKE.

Published
2022

13. Structural anomalies in a published NMR-derived structure of IRAK-M

Author

Sub Algemeen Scheikunde, Afd Scheikunde Algemeen, Poelman, Hessel, Ippel, Hans, Gürkan, Berke, Boelens, Rolf, Vriend, Gert, Veer, Cornelis van ‘t, Lutgens, Esther, Nicolaes, Gerry A.F., Sub Algemeen Scheikunde, Afd Scheikunde Algemeen, Poelman, Hessel, Ippel, Hans, Gürkan, Berke, Boelens, Rolf, Vriend, Gert, Veer, Cornelis van ‘t, Lutgens, Esther, and Nicolaes, Gerry A.F.

Published
2022

17. Ten Simples Rules on How to Organise a Bioinformatics Hackathon

Author

Hollmann, Susanne, primary, Regierer, Babette, additional, Attwood, Teresa K, additional, Gisel, Andreas, additional, Van Helden, Jacques, additional, Rossier, Gregoire, additional, Kersey, Paul J, additional, Korpelainen, Eija, additional, Vriend, Gert, additional, and Bongcam-Rudloff, Erik, additional

Published
2021
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21. Outer membrane phospholipase A's roles in Helicobacter pylori acid adaptation

Author

Vollan, Hilde S., Tannaes, Tone, Caugant, Dominique A., Vriend, Gert, and Bukholm, Geir

Subjects
Toleration -- Research, Stress (Physiology) -- Research, Phospholipases -- Research, Helicobacter pylori -- Research -- Genetic aspects -- Physiological aspects, Health
Abstract

Background The pH of the human gastric mucosa varies around 2.5 so that only bacteria with strong acidic stress tolerance can colonize it. The ulcer causing Helicobacter pylori thrives in the gastric mucosa. We analyse the roles of the key outer membrane protein OMPLA in its roles in acid tolerance. Results The homology model of Helicobacter pylori outer membrane phospholipase A (OMPLA) reveals a twelve stranded [beta]-barrel with a pore that allows molecules to pass with a diameter up to 4 Ã. Structure based multiple sequence alignments revealed the functional roles of many amino acids, and led to the suggestion that OMPLA has multiple functions. Besides its role as phospholipase it lets urea enter and ammonium exit the periplasm. Combined with an extensive literature study, our work leads to a comprehensive model for H. pylori's acid tolerance. This model is based on the conversion of urea into ammonium, and it includes multiple roles for OMPLA and involves two hitherto little studied membrane channels in the OMPLA operon. Conclusion The three-dimensional model of OMPLA predicts a transmembrane pore that can aid H. pylori's acid tolerance through urea influx and ammonium efflux. After urea passes through OMPLA into the periplasm, it passes through the pH-gated inner membrane channel UreI into the cytoplasm where urease hydrolyses it into NH.sub.3 and CO.sub.2. Most of the NH.sub.3 becomes NH.sub.4.sup.+ that is likely to need an inner membrane channel to reach the periplasm. Two genes that are co-regulated with OMPLA in gastric Helicobacter operons could aid this transport. The NH.sub.4.sup.+ that might leave the cell through the OMPLA pore has been implicated in H. pylor's pathogenesis. Keywords: Helicobacter pylori, Acid tolerance, Multifunctional OMPLA, Urea pathway, Author(s): Hilde S. Vollan[sup.1,2] , Tone Tannaes[sup.1] , Dominique A. Caugant[sup.2,3] , Gert Vriend[sup.4] and Geir Bukholm[sup.2,5] Background H. pylori survives in the human gastric mucosa Most bacterial proteins require [...]

Published
2017
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23. Class A GPCRs harness the energy of membrane potential to increase their sensitivity and selectivity

Author

Shalaeva, Daria N., Cherepanov, Dmitry A., Galperin, Michael Y., Vriend, Gert, and Mulkidjanian, Armen Y.

Subjects
Models, Molecular, Binding Sites, Cell Membrane, Sodium, Biological Transport, Active, Humans, Models, Theoretical, Article, Membrane Potentials, Protein Binding, Receptors, G-Protein-Coupled
Abstract

The human genome contains about 700 genes of G protein-coupled receptors (GPCRs) of class A; these seven-helical membrane proteins are the targets of almost half of all known drugs. In the middle of the helix bundle, crystal structures revealed a highly conserved sodium-binding site, which is connected with the extracellular side by a water-filled tunnel. This binding site contains a sodium ion in GPCRs crystallized in their inactive conformations, but not in GPCRs that were trapped in agonist-bound active conformations. The escape route of the sodium ion upon the inactive-to-active transition and its very direction, either into the cytoplasm or back outside the cell, have remained obscure. By modeling the available experimental data we show that the sodium gradient over the cell membrane would increase the sensitivity of GPCRs if their activation were thermodynamically coupled to the sodium ion translocation into the cytoplasm, but decrease it if the sodium ion retreats into the extracellular space upon receptor activation. The model quantitatively describes the available data on both activation and suppression of distinct GPCRs by membrane voltage. The model also predicts selective amplification of the signal from (endogenous) agonists if only they, but not their (partial) analogs, could induce sodium translocation. Comparative structure and sequence analyses of sodium-binding GPCRs indicate a key role for the conserved leucine residue in the second transmembrane helix (Leu2.46) in coupling sodium translocation to receptor activation. Hence, class A GPCRs appear to harness the energy of the transmembrane sodium potential to increase their sensitivity and selectivity.

Published
2019

24. Additional file 1: of The bio.tools registry of software tools and data resources for the life sciences

Author

Ison, Jon, Ienasescu, Hans, Chmura, Piotr, Rydza, Emil, Ménager, Hervé, Matúš Kalaš, Schwämmle, Veit, Grüning, Björn, Beard, Niall, Lopez, Rodrigo, Duvaud, Severine, Stockinger, Heinz, Persson, Bengt, Vařeková, Radka, Tomáš Raček, Jiří Vondrášek, Peterson, Hedi, Salumets, Ahto, Jonassen, Inge, Hooft, Rob, Nyrönen, Tommi, Valencia, Alfonso, Capella, Salvador, Gelpí, Josep, Zambelli, Federico, Babis Savakis, Leskošek, Brane, Rapacki, Kristoffer, Blanchet, Christophe, Jimenez, Rafael, Oliveira, Arlindo, Vriend, Gert, Collin, Olivier, Helden, Jacques, Løngreen, Peter, and Brunak, Søren

Subjects
FOS: Computer and information sciences, Sociology, 39999 Chemical Sciences not elsewhere classified, FOS: Chemical sciences, Science Policy, FOS: Biological sciences, 80699 Information Systems not elsewhere classified, Biochemistry, Molecular Biology, 69999 Biological Sciences not elsewhere classified, FOS: Sociology, Developmental Biology
Abstract

Review history. (DOCX 20 kb)

Published
2019
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28. Targeting CD40-Induced TRAF6 Signaling in Macrophages Reduces Atherosclerosis

Author

Seijkens, Tom T.P., primary, van Tiel, Claudia M., additional, Kusters, Pascal J.H., additional, Atzler, Dorothee, additional, Soehnlein, Oliver, additional, Zarzycka, Barbara, additional, Aarts, Suzanne A.B.M., additional, Lameijer, Marnix, additional, Gijbels, Marion J., additional, Beckers, Linda, additional, den Toom, Myrthe, additional, Slütter, Bram, additional, Kuiper, Johan, additional, Duchene, Johan, additional, Aslani, Maria, additional, Megens, Remco T.A., additional, van ‘t Veer, Cornelis, additional, Kooij, Gijs, additional, Schrijver, Roy, additional, Hoeksema, Marten A., additional, Boon, Louis, additional, Fay, Francois, additional, Tang, Jun, additional, Baxter, Samantha, additional, Jongejan, Aldo, additional, Moerland, Perry D., additional, Vriend, Gert, additional, Bleijlevens, Boris, additional, Fisher, Edward A., additional, Duivenvoorden, Raphael, additional, Gerdes, Norbert, additional, de Winther, Menno P.J., additional, Nicolaes, Gerry A., additional, Mulder, Willem J.M., additional, Weber, Christian, additional, and Lutgens, Esther, additional

Published
2018
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32. CorNet: Assigning function to networks of co-evolving residues by automated literature mining

Author

van den Bergh, Tom, primary, Tamo, Giorgio, additional, Nobili, Alberto, additional, Tao, Yifeng, additional, Tan, Tianwei, additional, Bornscheuer, Uwe T., additional, Kuipers, Remko K. P., additional, Vroling, Bas, additional, de Jong, René M., additional, Subramanian, Kalyanasundaram, additional, Schaap, Peter J., additional, Desmet, Tom, additional, Nidetzky, Bernd, additional, Vriend, Gert, additional, and Joosten, Henk-Jan, additional

Published
2017
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33. NewProt – a protein engineering portal

Author

Schwarte, Andreas, primary, Genz, Maika, additional, Skalden, Lilly, additional, Nobili, Alberto, additional, Vickers, Clare, additional, Melse, Okke, additional, Kuipers, Remko, additional, Joosten, Henk-Jan, additional, Stourac, Jan, additional, Bendl, Jaroslav, additional, Black, Jon, additional, Haase, Peter, additional, Baakman, Coos, additional, Damborsky, Jiri, additional, Bornscheuer, Uwe, additional, Vriend, Gert, additional, and Venselaar, Hanka, additional

Published
2017
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34. Facilities that make the PDB data collection more powerful.

Author

Lange, Joanna, Baakman, Coos, Pistorius, Arthur, Krieger, Elmar, Hooft, Rob, Joosten, Robbie P., and Vriend, Gert

Abstract

We describe a series of databases and tools that directly or indirectly support biomedical research on macromolecules, with focus on their applicability in protein structure bioinformatics research. DSSP, that determines secondary structures of proteins, has been updated to work well with extremely large structures in multiple formats. The PDBREPORT database that lists anomalies in protein structures has been remade to remove many small problems. These reports are now available as PDF‐formatted files with a computer‐readable summary. The VASE software has been added to analyze and visualize HSSP multiple sequence alignments for protein structures. The Lists collection of databases has been extended with a series of databases, most noticeably with a database that gives each protein structure a grade for usefulness in protein structure bioinformatics projects. The PDB‐REDO collection of reanalyzed and re‐refined protein structures that were solved by X‐ray crystallography has been improved by dealing better with sugar residues and with hydrogen bonds, and adding many missing surface loops. All academic software underlying these protein structure bioinformatics applications and databases are now publicly accessible, either directly from the authors or from the GitHub software repository. [ABSTRACT FROM AUTHOR]

Published
2020
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35. CorNet: Assigning function to networks of co-evolving residues by automated literature mining

Author

Van Den Bergh, Tom, Tamo, Giorgio, Nobili, Alberto, Tao, Yifeng, Tan, Tianwei, Bornscheuer, Uwe T., Kuipers, Remko K.P., Vroling, Bas, De Jong, René M., Subramanian, Kalyanasundaram, Schaap, Peter J., Desmet, Tom, Nidetzky, Bernd, Vriend, Gert, Joosten, Henk-Jan, Van Den Bergh, Tom, Tamo, Giorgio, Nobili, Alberto, Tao, Yifeng, Tan, Tianwei, Bornscheuer, Uwe T., Kuipers, Remko K.P., Vroling, Bas, De Jong, René M., Subramanian, Kalyanasundaram, Schaap, Peter J., Desmet, Tom, Nidetzky, Bernd, Vriend, Gert, and Joosten, Henk-Jan

Abstract

CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity. This finding allows to assign a function to residues for which no data is available yet in the literature. A mutant library was designed to mutate residues observed in a group of co-evolving residues predicted to be involved in enantioselectivity, but for which no literature data is available yet. The resulting set of mutations indeed showed many instances of increased enantioselectivity.

Published
2017

36. The EMBRACE web service collection

Author

Pettifer, Steve, Ison, Jon, Kalaš, Mat�š, Thorne, Dave, McDermott, Philip, Jonassen, Inge, Liaquat, Ali, Fern�ndez, Jos� M., Rodriguez, Jose M., Partners, INB, Pisano, David G., Blanchet, Christophe, Uludag, Mahmut, Rice, Peter, Bartaseviciute, Edita, Rapacki, Kristoffer, Hekkelman, Maarten, Sand, Olivier, Stockinger, Heinz, Clegg, Andrew B., Bongcam-Rudloff, Erik, Salzemann, Jean, Breton, Vincent, Attwood, Teresa K., Cameron, Graham, Vriend, Gert, Pettifer, Steve, Ison, Jon, Kalaš, Mat�š, Thorne, Dave, McDermott, Philip, Jonassen, Inge, Liaquat, Ali, Fern�ndez, Jos� M., Rodriguez, Jose M., Partners, INB, Pisano, David G., Blanchet, Christophe, Uludag, Mahmut, Rice, Peter, Bartaseviciute, Edita, Rapacki, Kristoffer, Hekkelman, Maarten, Sand, Olivier, Stockinger, Heinz, Clegg, Andrew B., Bongcam-Rudloff, Erik, Salzemann, Jean, Breton, Vincent, Attwood, Teresa K., Cameron, Graham, and Vriend, Gert

Abstract

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions

Published
2017

38. The role of the dopamine D1 receptor in social cognition : Studies using a novel genetic rat model

Author

Homberg, Judith R., Olivier, Jocelien D A, VandenBroeke, Marie, Youn, Jiun, Ellenbroek, Arabella K., Karel, Peter, Shan, Ling, Van Boxtel, Ruben, Ooms, Sharon, Balemans, Monique, Langedijk, Jacqueline, Muller, Mareike, Vriend, Gert, Cools, Alexander R., Cuppen, Edwin, Ellenbroek, Bart A., Homberg, Judith R., Olivier, Jocelien D A, VandenBroeke, Marie, Youn, Jiun, Ellenbroek, Arabella K., Karel, Peter, Shan, Ling, Van Boxtel, Ruben, Ooms, Sharon, Balemans, Monique, Langedijk, Jacqueline, Muller, Mareike, Vriend, Gert, Cools, Alexander R., Cuppen, Edwin, and Ellenbroek, Bart A.

Published
2016

39. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

40. The role of the dopamine D1 receptor in social cognition: Studies using a novel genetic rat model

Author

Hubrecht Institute with UMC, CMM Groep Cuppen, CMM, Circulatory Health, Cancer, Child Health, Brain, Homberg, Judith R., Olivier, Jocelien D A, VandenBroeke, Marie, Youn, Jiun, Ellenbroek, Arabella K., Karel, Peter, Shan, Ling, Van Boxtel, Ruben, Ooms, Sharon, Balemans, Monique, Langedijk, Jacqueline, Muller, Mareike, Vriend, Gert, Cools, Alexander R., Cuppen, Edwin, Ellenbroek, Bart A., Hubrecht Institute with UMC, CMM Groep Cuppen, CMM, Circulatory Health, Cancer, Child Health, Brain, Homberg, Judith R., Olivier, Jocelien D A, VandenBroeke, Marie, Youn, Jiun, Ellenbroek, Arabella K., Karel, Peter, Shan, Ling, Van Boxtel, Ruben, Ooms, Sharon, Balemans, Monique, Langedijk, Jacqueline, Muller, Mareike, Vriend, Gert, Cools, Alexander R., Cuppen, Edwin, and Ellenbroek, Bart A.

Published
2016

41. Tools and data services registry:a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

42. GPCRdb:an information system for G protein-coupled receptors

Author

Isberg, Vignir, Mordalski, Stefan, Munk, Christian, Rataj, Krzysztof, Harpsøe, Kasper, Hauser, Alexander S, Vroling, Bas, Bojarski, Andrzej J, Vriend, Gert, Gloriam, David E, Isberg, Vignir, Mordalski, Stefan, Munk, Christian, Rataj, Krzysztof, Harpsøe, Kasper, Hauser, Alexander S, Vroling, Bas, Bojarski, Andrzej J, Vriend, Gert, and Gloriam, David E

Abstract

Recent developments in G protein-coupled receptor (GPCR) structural biology and pharmacology have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing reference data, analysis tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iii) phylogenetic trees with receptor classification colour schemes. Under the hood, the entire GPCRdb front- and back-ends have been re-coded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.

Published
2016

43. GPCRdb: an information system for G protein-coupled receptors

Author

Isberg, Vignir, primary, Mordalski, Stefan, additional, Munk, Christian, additional, Rataj, Krzysztof, additional, Harpsøe, Kasper, additional, Hauser, Alexander S., additional, Vroling, Bas, additional, Bojarski, Andrzej J., additional, Vriend, Gert, additional, and Gloriam, David E., additional

Published
2016
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46. The bio.toolsregistry of software tools and data resources for the life sciences

Author

Ison, Jon, Ienasescu, Hans, Chmura, Piotr, Rydza, Emil, Ménager, Hervé, Kalaš, Matúš, Schwämmle, Veit, Grüning, Björn, Beard, Niall, Lopez, Rodrigo, Duvaud, Severine, Stockinger, Heinz, Persson, Bengt, Vařeková, Radka, Raček, Tomáš, Vondrášek, Jiří, Peterson, Hedi, Salumets, Ahto, Jonassen, Inge, Hooft, Rob, Nyrönen, Tommi, Valencia, Alfonso, Capella, Salvador, Gelpí, Josep, Zambelli, Federico, Savakis, Babis, Leskošek, Brane, Rapacki, Kristoffer, Blanchet, Christophe, Jimenez, Rafael, Oliveira, Arlindo, Vriend, Gert, Collin, Olivier, Helden, Jacques, Løngreen, Peter, and Brunak, Søren

Abstract

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.toolsnot only lists where to find resources, but also provides a wide variety of practical information.

Published
2019
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47. GPCRdb: an information system for G protein-coupled receptors

Author

Isberg, Vignir, primary, Mordalski, Stefan, additional, Munk, Christian, additional, Rataj, Krzysztof, additional, Harpsøe, Kasper, additional, Hauser, Alexander S., additional, Vroling, Bas, additional, Bojarski, Andrzej J., additional, Vriend, Gert, additional, and Gloriam, David E., additional

Published
2015
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49. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, Jon, primary, Rapacki, Kristoffer, additional, Ménager, Hervé, additional, Kalaš, Matúš, additional, Rydza, Emil, additional, Chmura, Piotr, additional, Anthon, Christian, additional, Beard, Niall, additional, Berka, Karel, additional, Bolser, Dan, additional, Booth, Tim, additional, Bretaudeau, Anthony, additional, Brezovsky, Jan, additional, Casadio, Rita, additional, Cesareni, Gianni, additional, Coppens, Frederik, additional, Cornell, Michael, additional, Cuccuru, Gianmauro, additional, Davidsen, Kristian, additional, Vedova, Gianluca Della, additional, Dogan, Tunca, additional, Doppelt-Azeroual, Olivia, additional, Emery, Laura, additional, Gasteiger, Elisabeth, additional, Gatter, Thomas, additional, Goldberg, Tatyana, additional, Grosjean, Marie, additional, Grüning, Björn, additional, Helmer-Citterich, Manuela, additional, Ienasescu, Hans, additional, Ioannidis, Vassilios, additional, Jespersen, Martin Closter, additional, Jimenez, Rafael, additional, Juty, Nick, additional, Juvan, Peter, additional, Koch, Maximilian, additional, Laibe, Camille, additional, Li, Jing-Woei, additional, Licata, Luana, additional, Mareuil, Fabien, additional, Mičetić, Ivan, additional, Friborg, Rune Møllegaard, additional, Moretti, Sebastien, additional, Morris, Chris, additional, Möller, Steffen, additional, Nenadic, Aleksandra, additional, Peterson, Hedi, additional, Profiti, Giuseppe, additional, Rice, Peter, additional, Romano, Paolo, additional, Roncaglia, Paola, additional, Saidi, Rabie, additional, Schafferhans, Andrea, additional, Schwämmle, Veit, additional, Smith, Callum, additional, Sperotto, Maria Maddalena, additional, Stockinger, Heinz, additional, Vařeková, Radka Svobodová, additional, Tosatto, Silvio C.E., additional, de la Torre, Victor, additional, Uva, Paolo, additional, Via, Allegra, additional, Yachdav, Guy, additional, Zambelli, Federico, additional, Vriend, Gert, additional, Rost, Burkhard, additional, Parkinson, Helen, additional, Løngreen, Peter, additional, and Brunak, Søren, additional

Published
2015
Full Text
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