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

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

Source: Genome Biology, Vol 20, Iss 1, Pp 1-4 (2019)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-019-1772-6; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/c83588b2872a4b119b058a97f0ced0f7

Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]

Authors: Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch

Source: F1000Research, Vol 6 (2017)

Subject Terms: Bioinformatics, Data Sharing, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/6-876/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/ae593f223a074427850b1fb626642ba4

Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway

Authors: Taraka Ramji Moturu, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, Sibu Simon

Source: Plants, Vol 9, Iss 3, p 299 (2020)

Subject Terms: small rna (smrnas), dawdle (ddl), tough (tgh), serrate (se/ars2), argonaute (ago), dicer-like (dcr/dcl), evolution, phylogeny, Botany, QK1-989

File Description: electronic resource

Relation: https://www.mdpi.com/2223-7747/9/3/299; https://doaj.org/toc/2223-7747

Access URL: https://doaj.org/article/70167f62efb243e598360b79794948d2

Top 10 metrics for life science software good practices [version 1; referees: 2 approved]

Authors: Haydee Artaza, Neil Chue Hong, Manuel Corpas, Angel Corpuz, Rob Hooft, Rafael C. Jimenez, Brane Leskošek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vařeková, Thomas Van Parys, Daniel Vaughan

Source: F1000Research, Vol 5 (2016)

Subject Terms: Bioinformatics, Health Systems & Services Research, Statistical Methodologies & Health Informatics, Medicine, Science

File Description: electronic resource

Relation: http://f1000research.com/articles/5-2000/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/2e7b172f4ba546acaf58f11cd4859fca

SugarSketcher: Quick and Intuitive Online Glycan Drawing

Authors: Davide Alocci, Pavla Suchánková, Renaud Costa, Nicolas Hory, Julien Mariethoz, Radka Svobodová Vařeková, Philip Toukach, Frédérique Lisacek

Source: Molecules, Vol 23, Iss 12, p 3206 (2018)

Subject Terms: carbohydrate, 2D structure, software, SNFG notation, Organic chemistry, QD241-441

File Description: electronic resource

Relation: https://www.mdpi.com/1420-3049/23/12/3206; https://doaj.org/toc/1420-3049

Access URL: https://doaj.org/article/8106e0cabbc548d8b9909e770c2a19d6

Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation.

Authors: Crina-Maria Ionescu, Radka Svobodová Vařeková, Jochen H M Prehn, Heinrich J Huber, Jaroslav Koča

Source: PLoS Computational Biology, Vol 8, Iss 6, p e1002565 (2012)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3375244?pdf=render; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/f91620ab245d4efb81c4291dad7d04d2

The Eighth Central European Conference 'Chemistry towards Biology': Snapshot

Authors: András Perczel (Laboratory of Structural Chemistry and Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eötvös Loránd University), Atanas Atanasov (Department of Pharmacognosy, Faculty of Life Sciences, University of Vienna), Vladimír Sklenář (Central European Institute of Technology, Masaryk University), Jiří Nováček (Central European Institute of Technology, Masaryk University), Veronika Papoušková (Central European Institute of Technology, Masaryk University), Pavel Kadeřávek (Central European Institute of Technology, Masaryk University), Lukáš Žídek (Central European Institute of Technology, Masaryk University), Henryk Kozłowski (Department of Biological Chemistry, Faculty of Chemistry, University of Wroclaw), Joanna Wątły (Department of Biological Chemistry, Faculty of Chemistry, University of Wroclaw), Aleksandra Hecel (Department of Biological Chemistry, Faculty of Chemistry, University of Wroclaw), Paulina Kołkowska (Department of Biological Chemistry, Faculty of Chemistry, University of Wroclaw), Jaroslav Koča (Central European Institute of Technology, Masaryk University), Radka Svobodová-Vařeková (Central European Institute of Technology, Masaryk University), Lukáš Pravda (Central European Institute of Technology, Masaryk University), David Sehnal (Central European Institute of Technology, Masaryk University), Vladimír Horský (Central European Institute of Technology, Masaryk University), Stanislav Geidl (Central European Institute of Technology, Masaryk University), Ricardo Enriz (Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis), Pavel Matějka (Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague), Adéla Jeništová (Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague), Marcela Dendisová (Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague), Alžběta Kokaislová (Department of Physical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, Prague), Volkmar Weissig (Department of Medical Chemistry, College of Pharmacy Glendale, Midwestern University), Mark Olsen (Department of Medical Chemistry, College of Pharmacy Glendale, Midwestern University), Aidan Coffey (Department of Biological Sciences, Cork Institute of Technology), Jude Ajuebor (Department of Biological Sciences, Cork Institute of Technology), Ruth Keary (Department of Biological Sciences, Cork Institute of Technology), Marta Sanz-Gaitero (Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia, Spain), Mark van Raaij (Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia, Spain), Olivia McAuliffe (Biotechnology Department, Teagasc, Moorepark Food Research Centre), Birgit Waltenberger (Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck), Andrei Mocan (Department of Pharmaceutical Botany, Iuliu Hațieganu University of Medicine and Pharmacy), Karel Šmejkal (Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno), Elke Heiss (Department of Pharmacognosy, Faculty of Life Sciences, University of Vienna), Marc Diederich (Department of Pharmacy, College of Pharmacy, Seoul National University), Robert Musioł (Institute of Chemistry, University of Silesia), Janez Košmrlj (Faculty of Chemistry and Chemical Technology, University of Ljubljana), Jarosław Polański (Institute of Chemistry, University of Silesia), Josef Jampílek (Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University)

Availability: http://data.europeana.eu/aggregation/europeana/1300/https___phaidra_univie_ac_at_o_533928

Predicting pKaValues of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes.

Authors: Radka Svobodová Vařeková¹, Stanislav Geidl¹, Crina-Maria Ionescu¹, Ondřej Skřehota¹, Michal Kudera¹, David Sehnal¹, Tomáš Bouchal¹, Ruben Abagyan¹, Heinrich J. Huber¹, Jaroslav Koča¹

Source: Journal of Chemical Information & Modeling; Aug2011, Vol. 51 Issue 8, p1795-1806, 12p

The Eighth Central European Conference 'Chemistry towards Biology': Snapshot

Authors: András Perczel, Atanas G. Atanasov, Vladimír Sklenář, Jiří Nováček, Veronika Papoušková, Pavel Kadeřávek, Lukáš Žídek, Henryk Kozłowski, Joanna Wątły, Aleksandra Hecel, Paulina Kołkowska, Jaroslav Koča, Radka Svobodová-Vařeková, Lukáš Pravda, David Sehnal, Vladimír Horský, Stanislav Geidl, Ricardo D. Enriz, Pavel Matějka, Adéla Jeništová, Marcela Dendisová, Alžběta Kokaislová, Volkmar Weissig, Mark Olsen, Aidan Coffey, Jude Ajuebor, Ruth Keary, Marta Sanz-Gaitero, Mark J. van Raaij, Olivia McAuliffe, Birgit Waltenberger, Andrei Mocan, Karel Šmejkal, Elke H. Heiss, Marc Diederich, Robert Musioł, Janez Košmrlj, Jarosław Polański, Josef Jampílek

Source: Molecules, Vol 21, Iss 10, p 1381 (2016)

Subject Terms: drug design, targeting, chemical biology, biological chemistry, proteins and nucleic acids, natural compounds, synthesis, biomaterials, nanoparticles, ADME, drug delivery systems, Organic chemistry, QD241-441

File Description: electronic resource

Relation: http://www.mdpi.com/1420-3049/21/10/1381; https://doaj.org/toc/1420-3049

Access URL: https://doaj.org/article/3da4107db6eb446cb4b24cd5e31b819b