PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

por Sehnal, David, Pravda, Lukáš, Svobodová Vařeková, Radka, Ionescu, Crina-Maria, Koča, Jaroslav
Publicado 2015

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

por Ionescu, Crina-Maria, Svobodová Vařeková, Radka, Prehn, Jochen H. M., Huber, Heinrich J., Koča, Jaroslav
Publicado 2012

Validation of ligands in macromolecular structures determined by X-ray crystallography

por Smart, Oliver S., Horský, Vladimír, Gore, Swanand, Svobodová Vařeková, Radka, Bendová, Veronika, Kleywegt, Gerard J., Velankar, Sameer
Publicado 2018

Worldwide Protein Data Bank validation information: usage and trends

por Smart, Oliver S., Horský, Vladimír, Gore, Swanand, Svobodová Vařeková, Radka, Bendová, Veronika, Kleywegt, Gerard J., Velankar, Sameer
Publicado 2018

High-quality and universal empirical atomic charges for chemoinformatics applications

por Geidl, Stanislav, Bouchal, Tomáš, Raček, Tomáš, Svobodová Vařeková, Radka, Hejret, Václav, Křenek, Aleš, Abagyan, Ruben, Koča, Jaroslav
Publicado 2015

ChannelsDB: database of biomacromolecular tunnels and pores

por Pravda, Lukáš, Sehnal, David, Svobodová Vařeková, Radka, Navrátilová, Veronika, Toušek, Dominik, Berka, Karel, Otyepka, Michal, Koča, Jaroslav
Publicado 2018

Anatomy of enzyme channels

por Pravda, Lukáš, Berka, Karel, Svobodová Vařeková, Radka, Sehnal, David, Banáš, Pavel, Laskowski, Roman A, Koča, Jaroslav, Otyepka, Michal
Publicado 2014

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

por Pravda, Lukáš, Sehnal, David, Toušek, Dominik, Navrátilová, Veronika, Bazgier, Václav, Berka, Karel, Svobodová Vařeková, Radka, Koča, Jaroslav, Otyepka, Michal
Publicado 2018

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

por Sehnal, David, Svobodová Vařeková, Radka, Berka, Karel, Pravda, Lukáš, Navrátilová, Veronika, Banáš, Pavel, Ionescu, Crina-Maria, Otyepka, Michal, Koča, Jaroslav
Publicado 2013

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank

por Sehnal, David, Svobodová Vařeková, Radka, Pravda, Lukáš, Ionescu, Crina-Maria, Geidl, Stanislav, Horský, Vladimír, Jaiswal, Deepti, Wimmerová, Michaela, Koča, Jaroslav
Publicado 2014

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

por Raček, Tomáš, Pazúriková, Jana, Svobodová Vařeková, Radka, Geidl, Stanislav, Křenek, Aleš, Falginella, Francesco Luca, Horský, Vladimír, Hejret, Václav, Koča, Jaroslav
Publicado 2016

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

por Ionescu, Crina-Maria, Sehnal, David, Falginella, Francesco L., Pant, Purbaj, Pravda, Lukáš, Bouchal, Tomáš, Svobodová Vařeková, Radka, Geidl, Stanislav, Koča, Jaroslav
Publicado 2015

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

por Berka, Karel, Hanák, Ondřej, Sehnal, David, Banáš, Pavel, Navrátilová, Veronika, Jaiswal, Deepti, Ionescu, Crina-Maria, Svobodová Vařeková, Radka, Koča, Jaroslav, Otyepka, Michal
Publicado 2012

Top 10 metrics for life science software good practices

por Artaza, Haydee, Chue Hong, Neil, Corpas, Manuel, Corpuz, Angel, Hooft, Rob, Jimenez, Rafael C., Leskošek, Brane, Olivier, Brett G., Stourac, Jan, Svobodová Vařeková, Radka, Van Parys, Thomas, Vaughan, Daniel
Publicado 2016

PDBe: improved findability of macromolecular structure data in the PDB

por Armstrong, David R, Berrisford, John M, Conroy, Matthew J, Gutmanas, Aleksandras, Anyango, Stephen, Choudhary, Preeti, Clark, Alice R, Dana, Jose M, Deshpande, Mandar, Dunlop, Roisin, Gane, Paul, Gáborová, Romana, Gupta, Deepti, Haslam, Pauline, Koča, Jaroslav, Mak, Lora, Mir, Saqib, Mukhopadhyay, Abhik, Nadzirin, Nurul, Nair, Sreenath, Paysan-Lafosse, Typhaine, Pravda, Lukas, Sehnal, David, Salih, Osman, Smart, Oliver, Tolchard, James, Varadi, Mihaly, Svobodova-Vařeková, Radka, Zaki, Hossam, Kleywegt, Gerard J, Velankar, Sameer
Publicado 2020

The Eighth Central European Conference “Chemistry towards Biology”: Snapshot †

por Perczel, András, Atanasov, Atanas G., Sklenář, Vladimír, Nováček, Jiří, Papoušková, Veronika, Kadeřávek, Pavel, Žídek, Lukáš, Kozłowski, Henryk, Wątły, Joanna, Hecel, Aleksandra, Kołkowska, Paulina, Koča, Jaroslav, Svobodová-Vařeková, Radka, Pravda, Lukáš, Sehnal, David, Horský, Vladimír, Geidl, Stanislav, Enriz, Ricardo D., Matějka, Pavel, Jeništová, Adéla, Dendisová, Marcela, Kokaislová, Alžběta, Weissig, Volkmar, Olsen, Mark, Coffey, Aidan, Ajuebor, Jude, Keary, Ruth, Sanz-Gaitero, Marta, van Raaij, Mark J., McAuliffe, Olivia, Waltenberger, Birgit, Mocan, Andrei, Šmejkal, Karel, Heiss, Elke H., Diederich, Marc, Musioł, Robert, Košmrlj, Janez, Polański, Jarosław, Jampílek, Josef
Publicado 2016

Four simple recommendations to encourage best practices in research software

por Jiménez, Rafael C., Kuzak, Mateusz, Alhamdoosh, Monther, Barker, Michelle, Batut, Bérénice, Borg, Mikael, Capella-Gutierrez, Salvador, Chue Hong, Neil, Cook, Martin, Corpas, Manuel, Flannery, Madison, Garcia, Leyla, Gelpí, Josep Ll., Gladman, Simon, Goble, Carole, González Ferreiro, Montserrat, Gonzalez-Beltran, Alejandra, Griffin, Philippa C., Grüning, Björn, Hagberg, Jonas, Holub, Petr, Hooft, Rob, Ison, Jon, Katz, Daniel S., Leskošek, Brane, López Gómez, Federico, Oliveira, Luis J., Mellor, David, Mosbergen, Rowland, Mulder, Nicola, Perez-Riverol, Yasset, Pergl, Robert, Pichler, Horst, Pope, Bernard, Sanz, Ferran, Schneider, Maria V., Stodden, Victoria, Suchecki, Radosław, Svobodová Vařeková, Radka, Talvik, Harry-Anton, Todorov, Ilian, Treloar, Andrew, Tyagi, Sonika, van Gompel, Maarten, Vaughan, Daniel, Via, Allegra, Wang, Xiaochuan, Watson-Haigh, Nathan S., Crouch, Steve
Publicado 2017