doc. RNDr. Karel Berka, Ph.D.

2023

• ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era

  ŠPAČKOVÁ Anna VÁVRA Ondřej RAČEK Tomáš BAZGIER Václav SEHNAL David DAMBORSKÝ Jiří SVOBODOVÁ Radka BERKA Karel

  Conference abstract

  Year: 2023, type: Conference abstract

• Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations

  CHARESHNEU Aliaksei MIDLIK Adam IONESCU Crina-Maria ROSE Alexander HORSKÝ Vladimír CANTARA Alessio SVOBODOVÁ Radka BERKA Karel SEHNAL David

  Article in Periodical

  Nucleic Acids Research, year: 2023, volume: 51, edition: W1, DOI

• New ways of protein family visualization in AlphaFold era

  SVOBODOVÁ Radka BERKA Karel HUTAŘOVÁ VAŘEKOVÁ Ivana RAČEK Tomáš SCHINDLER Ondřej

  Appeared in Conference without Proceedings

  Year: 2023, type: Appeared in Conference without Proceedings

• αCharges: partial atomic charges for AlphaFold structures in high quality

  SCHINDLER Ondřej BERKA Karel CANTARA Alessio KŘENEK Aleš TICHÝ Dominik RAČEK Tomáš SVOBODOVÁ Radka

  Article in Periodical

  Nucleic Acids Research, year: 2023, volume: 51, edition: W1, DOI

2022

• OverProt: secondary structure consensus for protein families

  MIDLIK Adam HUTAŘOVÁ VAŘEKOVÁ Ivana HUTAŘ Jan CHARESHNEU Aliaksei BERKA Karel SVOBODOVÁ Radka

  Article in Periodical

  Bioinformatics, year: 2022, volume: 38, edition: 14, DOI

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

• 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

• QM-like partial atomic charges for proteins available online

  SCHINDLER Ondřej RAČEK Tomáš SVOBODOVÁ Radka BERKA Karel

  Conference abstract

  Year: 2021, type: Conference abstract

2020

• Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

  RAČEK Tomáš SCHINDLER Ondřej TOUŠEK Dominik HORSKÝ Vladimír BERKA Karel KOČA Jaroslav SVOBODOVÁ Radka

  Article in Periodical

  Nucleic acids research, year: 2020, volume: 48, edition: W1, DOI

• SQE charge calculation and its applicability for proteins

  SCHINDLER Ondřej RAČEK Tomáš SVOBODOVÁ Radka BERKA Karel KOČA Jaroslav

  Conference abstract

  Year: 2020, type: Conference abstract