doc. RNDr. Radka Svobodová, Ph.D.

2022

• PDBe-KB: collaboratively defining the biological context of structural data

  VARADI Mihaly ANYANGO Stephen ARMSTRONG David BERRISFORD John CHOUDHARY Preeti DESHPANDE Mandar NADZIRIN Nurul NAIR Sreenatha S. PRAVDA Lukas TANWEER Ahsan AL-LAZIKANI Bissan ANDREINI Claudia BARTON Geoffrey J. BEDNÁŘ David BERKA Karel BLUNDELL Tom BROCK Kelly P. MARIA CARAZO Jose DAMBORSKÝ Jiří DAVID Alessia DEY Sucharita DUNBRACK Roland RECIO Fernandez Juan FRATERNALI Franca GIBSON Toby HELMER-CITTERICH Manuela HOKSZA David HOPF Thomas JAKUBEC David KANNAN Natarajan KRIVAK Radoslav KUMAR Manjeet LEVY Emmanuel D. LONDON Nir MACIAS Jose Ramon SRIVATSAN Madhusudhan M. MARKS Debora S. MARTENS Lennart MCGOWAN Stuart A. MCGREIG Jake E. MODI Vivek PARRA Gonzalo R. PEPE Gerardo PIOVESAN Damiano PRILUSKY Jaime PUTIGNANO Valeria RADUSKY Leandro G. RAMASAMY Pathmanaban RAUSCH Atilio O. REUTER Nathalie RODRIGUEZ Luis A. ROLLINS Nathan J. ROSATO Antonio SERRANO Luis SINGH Gulzar SKODA Petr SORZANO Carlos Oscar S. ŠTOURAČ Jan SULKOWSKA Joanna I. SVOBODOVÁ Radka TICHSHENKO Natalia TOSATTO Silvio C. E. VRANKEN Wim WASS Mark N. XUE Dandan ZAIDMAN Daniel THORNTON Janet STERNBERG Michael ORENGO Christine VELANKAR Sameer

  Article in Periodical

  Nucleic acids research, year: 2022, volume: 50, edition: D1, DOI

• Prediction of QM-like partial atomic charges for alphafold

  SCHINDLER Ondřej RAČEK Tomáš SVOBODOVÁ Radka

  Appeared in Conference without Proceedings

  Year: 2022, type: Appeared in Conference without Proceedings

• QM-like partial atomic charges for AlphaFold available online

  SCHINDLER Ondřej RAČEK Tomáš JELÍNEK Kamil SVOBODOVÁ Radka

  Conference abstract

  Year: 2022, type: Conference abstract

• Validation of cycle conformation in small molecules

  BUČEKOVÁ Gabriela DOSHCHENKO Viktoriia CHARESHNEU Aliaksei SVOBODOVÁ Radka

  Conference abstract

  Year: 2022, type: Conference abstract

2021

• 2DProts: database of family-wide protein secondary structure diagrams

  HUTAŘOVÁ VAŘEKOVÁ Ivana HUTAŘ Jan MIDLIK Adam HORSKÝ Vladimír HLADKÁ Eva SVOBODOVÁ Radka BERKA Karel

  Article in Periodical

  Bioinformatics, year: 2021, volume: 37, edition: 23, DOI

• CATH: increased structural coverage of functional space

  SILLITOE Ian BORDIN Nicola DAWSON Natalie WAMAN Vaishali P. ASHFORD Paul SCHOLES Harry M. PANG Camilla S.M. WOODRIDGE Laurel RAUER Clemens SEN Neeladri ABBASIAN Mahnaz LE CORNU Sean LAM Su Datt BERKA Karel HUTAŘOVÁ VAŘEKOVÁ Ivana SVOBODOVÁ Radka LEES Jon ORENGO Christine A.

  Article in Periodical

  Nucleic Acids Research, year: 2021, volume: 49, edition: D1, DOI

• Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

  SEHNAL David BITTRICH S. DESHPANDE M. SVOBODOVÁ Radka BERKA K. BAZGIER V. VELANKAR S. BURLEY S.K. KOČA Jaroslav ROSE A.S.

  Article in Periodical

  Nucleic acids research, year: 2021, volume: 49, edition: W1, DOI

• Optimized SQE atomic charges for peptides accessible via a web application

  SCHINDLER Ondřej RAČEK Tomáš MARŠAVELSKI Aleksandra KOČA Jaroslav BERKA Karel SVOBODOVÁ Radka

  Article in Periodical

  Journal of Cheminformatics, year: 2021, volume: 13, edition: 1, DOI

• Partial atomic charges for proteins

  SCHINDLER Ondřej RAČEK Tomáš MARŠAVELSKI Aleksandra SVOBODOVÁ Radka KOČA Jaroslav

  Appeared in Conference without Proceedings

  Year: 2021, type: Appeared in Conference without Proceedings

• QM-like partial atomic charges for proteins available online

  SCHINDLER Ondřej RAČEK Tomáš SVOBODOVÁ Radka BERKA Karel

  Conference abstract

  Year: 2021, type: Conference abstract