Publications

2016

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

  RAČEK Tomáš PAZÚRIKOVÁ Jana SVOBODOVÁ VAŘEKOVÁ Radka GEIDL Stanislav KŘENEK Aleš FALGINELLA Francesco Luca HORSKÝ Vladimír HEJRET Václav KOČA Jaroslav

  Article in Periodical

  Journal of Cheminformatics, year: 2016, volume: 8, edition: October, DOI

• Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

  ADAMS Paul D. AERTGEERTS Kathleen BAUER Cary BELL Jeffrey A. BERMAN Helen M. BHAT Talapady N. BLANEY Jeff M. BOLTON Evan BRICOGNE Gerard BROWN David BURLEY Stephen K. CASE David A. CLARK Kirk L. DARDEN Tom EMSLEY Paul FEHER Victoria A. FENG Zukang GROOM Colin R. HARRIS Seth F. HENDLE Jorg HOLDER Thomas JOACHIMIAK Andrzej KLEYWEGT Gerard J. KROJER Tobias MARCOTRIGIANO Joseph MARK Alan E. MARKLEY John L. MILLER Matthew MINOR Wladek MONTELIONE Gaetano T. MURSHUDOV Garib NAKAGAWA Atsushi NAKAMURA Haruki NICHOLLS Anthony NICKLAUS Marc NOLTE Robet T. PADYANA Anil K. PEISHOFF Catherine E. PIENIAZEK Susan READ Randy J. SHAO Chenghua SHERIFF Steven SMART Oliver SOISSON Stephen SPURLINO John STOUCH Terry SVOBODOVÁ VAŘEKOVÁ Radka TEMPEL Wolfram TERWILLIGER Thomas C. TRONRUD Dale VELANKAR Sameer WARD Suzanna C. WARREN Gregory L. WESTBROOK John D. WILLIAMS Pamela YANG Huanwang YOUNG Jasmine

  Article in Periodical

  Structure, year: 2016, volume: 24, edition: 4, DOI

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

  PERCZEL András ATANASOV Atanas G. SKLENÁŘ Vladimír NOVÁČEK Jiří PAPOUŠKOVÁ Veronika KADEŘÁVEK Pavel ŽÍDEK Lukáš KOZLOWSKI Henryk WATLY Joanna HECEL Aleksandra KOLKOWSKA 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 MUSIOL Robert KOŠMRLJ Janez POLANSKI Jaroslaw JAMPÍLEK Josef

  Article in Periodical

  MOLECULES, year: 2016, volume: 21, edition: 10, DOI

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

  ISON Jon RAPACKI Kristoffer MENAGER Herve KALAS Matus RYDZA Emil CHMURA Piotr ANTHON Christian BEARD Niall BERKA Karel BOLSER Dan BOOTH Tim BRETAUDEAU Anthony BREZOVSKÝ Jan CASADIO Rita CESARENI Gianni COPPENS Frederik CORNELL Michael CUCCURU Gianmauro DAVIDSEN Kristian DELLA VEDOVA Gianluca DOGAN Tunca DOPPELT-AZEROUAL Olivia EMERY Laura GASTEIGER Elisabeth GATTER Thomas GOLDBERG Tatyana GROSJEAN Marie GRUNING Bjoern 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 MICETIC Ivan FRIBORG Rune Mollegaard MORETTI Sebastien MORRIS Chris MOLLER Steffen NENADIC Aleksandra PETERSON Hedi PROFITI Giuseppe RICE Peter ROMANO Paolo RONCAGLIA Paola SAIDI Rabie SCHAFFERHANS Andrea SCHWAMMLE Veit SMITH Callum SPEROTTO Maria Maddalena STOCKINGER Heinz SVOBODOVÁ VAŘEKOVÁ Radka TOSATTO Silvio C. E. DE LA TORRE Victor UVA Paolo VIA Allegra YACHDAV Guy ZAMBELLI Federico VRIEND Gert ROST Burkhard PARKINSON Helen LONGREEN Peter BRUNAK Soren

  Article in Periodical

  Nucleic Acids Research, year: 2016, volume: 44, edition: D1, DOI

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

  ARTAZA H. HONG N. C. CORPAS M. CORPUZ A. HOOFT R. JIMENEZ R. C. LESKOŠEK B. OLIVIER B. G. STOURAC J. SVOBODOVÁ VAŘEKOVÁ Radka VAN PARYS T. VAUGHAN D.

  Article in Periodical

  F1000Research, year: 2016, volume: 5, edition: August, DOI

2015

• AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules

  IONESCU Crina-Maria SEHNAL David FALGINELLA Francesco Luca PANT Purbaj PRAVDA Lukáš BOUCHAL Tomáš SVOBODOVÁ VAŘEKOVÁ Radka GEIDL Stanislav KOČA Jaroslav

  Article in Periodical

  Journal of Cheminformatics, year: 2015, volume: 7, edition: 50, DOI

• High-quality and universal empirical atomic charges for chemoinformatics applications

  GEIDL Stanislav BOUCHAL Tomáš RAČEK Tomáš SVOBODOVÁ VAŘEKOVÁ Radka HEJRET Václav KŘENEK Aleš ABAGYAN Ruben KOČA Jaroslav

  Article in Periodical

  Journal of Cheminformatics, year: 2015, volume: 7, edition: DEC, DOI

• How Does the Methodology of 3D Structure Preparation Influence the Quality of pK(a) Prediction?

  GEIDL Stanislav SVOBODOVÁ VAŘEKOVÁ Radka BENDOVÁ Veronika PETRUSEK Lukáš IONESCU Crina-Maria JURKA Zdeněk ABAGYAN Ruben A. KOČA Jaroslav

  Article in Periodical

  Journal of Chemical Information and Modeling, year: 2015, volume: 55, edition: 6, DOI

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

  SEHNAL David PRAVDA Lukáš SVOBODOVÁ VAŘEKOVÁ Radka IONESCU Crina-Maria KOČA Jaroslav

  Article in Periodical

  Nucleic Acids Research, year: 2015, volume: 43, edition: W1, DOI

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

  SEHNAL David SVOBODOVÁ VAŘEKOVÁ Radka PRAVDA Lukáš IONESCU Crina-Maria GEIDL Stanislav HORSKÝ Vladimír JAISWAL Deepti WIMMEROVÁ Michaela KOČA Jaroslav

  Article in Periodical

  Nucleic Acids Research, year: 2015, volume: 43, edition: D1, DOI